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Gene transcriptions/A1BG/Core promoters

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The diagram shows an overview of the four core promoter elements B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), with their respective consensus sequences and their distance from the transcription start site.[1] Credit: Jennifer E.F. Butler & James T. Kadonaga.

The core promoter is the minimal portion of the promoter required to properly initiate transcription.[2] The core promoter is approximately -34 nts upstream from the TSS. "Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)".[3][4]

GC content

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Approximately "76% of human core promoters lack TATA-like elements, have a high GC content, and are enriched in Sp1 binding sites."[5] The core promoter for A1BG does not have a high GC content.

CpG islands typically occur at or near the transcription start site of genes, particularly housekeeping genes, in vertebrates.[6]

The number of CG or GC pairs near the TSS for A1BG appears to be low (closer to ~6 % rather than ~60 %).

ATA boxes

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Main resources: Gene transcriptions/Boxes/ATA and ATA boxes

For the Basic programs (starting with SuccessablesATA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesATA--.bas, looking for 3'-AATAAA-5', 1, 3'-AATAAA-5', 1726,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesATA-+.bas, looking for 3'-AATAAA-5', 0,
  3. positive strand in the negative direction is SuccessablesATA+-.bas, looking for 3'-AATAAA-5', 3, 3'-AATAAA-5', 3014, 3'-AATAAA-5', 3335, 3'-AATAAA-5', 4072,
  4. positive strand in the positive direction is SuccessablesATA++.bas, looking for 3'-AATAAA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesATAc--.bas, looking for 3'-TTATTT-5', 3, 3'-TTATTT-5', 3014, 3'-TTATTT-5', 3335, 3'-TTATTT-5', 4072,
  6. complement, negative strand, positive direction is SuccessablesATAc-+.bas, looking for 3'-TTATTT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesATAc+-.bas, looking for 3'-TTATTT-5', 1, 3'-TTATTT-5', 1726,
  8. complement, positive strand, positive direction is SuccessablesATAc++.bas, looking for 3'-TTATTT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesATAci--.bas, looking for 3'-TTTATT-5', 5, 3'-TTTATT-5', 3013, 3'-TTTATT-5', 3334, 3'-TTTATT-5', 4071, 3'-TTTATT-5', 4075, 3'-TTTATT-5', 4221,
  10. inverse complement, negative strand, positive direction is SuccessablesATAci-+.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 703,
  11. inverse complement, positive strand, negative direction is SuccessablesATAci+-.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 4537,
  12. inverse complement, positive strand, positive direction is SuccessablesATAci++.bas, looking for 3'-TTTATT-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesATAi--.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 4537,
  14. inverse, negative strand, positive direction, is SuccessablesATAi-+.bas, looking for 3'-AAATAA-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesATAi+-.bas, looking for 3'-AAATAA-5', 5, 3'-AAATAA-5', 3013, 3'-AAATAA-5', 3334, 3'-AAATAA-5', 4071, 3'-AAATAA-5', 4075, 3'-AAATAA-5', 4221,
  16. inverse, positive strand, positive direction, is SuccessablesATAi++.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 703.

B recognition elements

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Main resources: Gene transcriptions/Elements/Factor II B recognition and B recognition elements

Consensus sequence on the template strand for the B recognition element is 3'-G/C-G/C-G/A-C-G-C-C-5'.

The consensus sequence is 5’-G/C G/C G/A C G C C-3’.[7]

The general consensus sequence using degenerate nucleotides is 5’-SSRCGCC-3’, where S = G or C and R = A or G.[5]

For the Basic programs (starting with Successables.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction is SuccessablesBRE--.bas, looking for 3'-G/C-G/C-G/A-C-G-C-C-5', 3, 3'-CCACGCC-5' at 380, 3'-CCGCGCC-5' at 1762, and 3'-CCACGCC-5' at 2197.
  2. negative strand in the positive direction is SuccessablesBRE-+.bas, looking for 3'-G/C-G/C-G/A-C-G-C-C-5', 3, 3'-GCACGCC-5', 1302, 3'-GGACGCC-5', 1672, 3'-GGGCGCC-5', 1769,
  3. positive strand in the negative direction is SuccessablesBRE+-.bas, looking for 3'-G/C-G/C-G/A-C-G-C-C-5', 0,
  4. positive strand in the positive direction is SuccessablesBRE++.bas, looking for 3'-G/C-G/C-G/A-C-G-C-C-5', 3, 3'-CCACGCC-5', 489, 3'-CGACGCC-5', 1033, 3'-CCACGCC-5', 1764,
  5. complement, negative strand, negative direction is SuccessablesBREc--.bas, looking for 3'-G/C-G/C-C/T-G-C-G-G-5', 1, 3'-CCTGCGG-5' at 1153,
  6. complement, negative strand, positive direction is SuccessablesBREc-+.bas, looking for 3'-G/C-G/C-C/T-G-C-G-G-5', 3, 3'-GGTGCGG-5', 489, 3'-GCTGCGG-5', 1033, 3'-GGTGCGG-5', 1764,
  7. complement, positive strand, negative direction is SuccessablesBREc+-.bas, looking for 3'-G/C-G/C-C/T-G-C-G-G-5', 3, 3'-GGTGCGG-5' at 380, 3'-GGCGCGG-5' at 1762, and 3'-GGTGCGG-5' at 2197,
  8. complement, positive strand, negative direction is SuccessablesBREc++.bas, looking for 3'-G/C-G/C-C/T-G-C-G-G-5', 3, 3'-CGTGCGG-5', 1302, 3'-CCTGCGG-5', 1672, 3'-CCCGCGG-5', 1769,
  9. inverse complement, negative strand, negative direction is SuccessablesBREci--.bas, looking for 3'-G-G-C-G-C/T-G/C-G/C-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesBREci-+.bas, looking for 3'-G-G-C-G-C/T-G/C-G/C-5', 1, 3'-GGCGCCC-5', 1770,
  11. inverse complement, positive strand, negative direction is SuccessablesBREci+-.bas, looking for 3'-G-G-C-G-C/T-G/C-G/C-5', 4, 3'-GGCGTGG-5' at 1244, 3'-GGCGCGG-5' at 1762, 3'-GGCGTGG-5' at 1897, and 3'-GGCGTGG-5' at 3047,
  12. inverse complement, positive strand, positive direction is SuccessablesBREci++.bas, looking for 3'-G-G-C-G-C/T-G/C-G/C-5', 4, 3'-GGCGCGC-5', 682, 3'-GGCGCCG-5', 1338, 3'-GGCGCCG-5', 1438, 3'-GGCGTGG-5', 2566,
  13. inverse, negative strand, negative direction, is SuccessablesBREi--.bas, looking for 3'-C-C-G-C-G/A-G/C-G/C-5', 4, 3'-CCGCACC-5' at 1244, 3'-CCGCGCC-5' at 1762, 3'-CCGCACC-5' at 1897, and 3'-CCGCACC-5' at 3047,
  14. inverse, negative strand, positive direction, is SuccessablesBREi-+.bas, looking for 3'-C-C-G-C-G/A-G/C-G/C-5', 4, 3'-CCGCGCG-5', 682, 3'-CCGCGGC-5', 1338, 3'-CCGCGGC-5', 1438, 3'-CCGCACC-5', 2566,
  15. inverse, positive strand, negative direction, is SuccessablesBREi+-.bas, looking for 3'-C-C-G-C-G/A-G/C-G/C-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesBREi++.bas, looking for 3'-C-C-G-C-G/A-G/C-G/C-5', 1, 3'-CCGCGGG-5', 1770.

CAAT boxes

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Main resources: Gene transcriptions/Boxes/CAAT and CAAT boxes

A CCAAT box (also sometimes abbreviated a CAAT box or CAT box) is a distinct pattern of nucleotides along the template strand of DNA in eukaryotes.

On the template strand, the CAAT box consensus sequence is 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5'.

For the Basic programs (starting with SuccessablesCAAT.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. CAAT - 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', -- there are zero, -+ there are zero, +- there are zero, ++ there are zero.
  2. CAAT - 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', complement, -- there are zero, -+ there are zero, +- there are zero, and ++ there are zero.
  3. CAAT - 3'-(A/G)-C-T-A-A-C-C-(A/G)-(A/G)-(C/T)-5', inverse, -- there are zero, -+ there are zero, +- there are zero, and ++ there are zero.
  4. CAAT - 3'-(C/T)-G-A-T-T-G-G-(C/T)-(C/T)-(A/G)-5', complement inverse, -- there are zero, -+ there are zero, +- there are zero, and ++ there are zero.

With each SuccessablesCAAT.bas extended from 958 to 4445 nts starting just beyond ZNF497, there are no changes in results.

C and D boxes

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Main resources: Gene transcriptions/Boxes/C/Ds and C and D boxes

Substituting T for U yields C box = 3'-AGTAGT-5' and D box = 3'-AGTCTG-5' in the transcription direction on the template strand.

C box

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C box = 3'-AGTAGT-5'

For the Basic programs (starting with SuccessablesCbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCbox--.bas, looking for 3'-AGTAGT-5', 4, 3'-AGTAGT-5', 2888, 3'-AGTAGT-5', 2944, 3'-AGTAGT-5', 3418, 3'-AGTAGT-5', 3521,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCbox-+.bas, looking for 3'-AGTAGT-5', 0,
  3. positive strand in the negative direction is SuccessablesCbox+-.bas, looking for 3'-AGTAGT-5', 0,
  4. positive strand in the positive direction is SuccessablesCbox++.bas, looking for 3'-AGTAGT-5', 1, 3'-AGTAGT-5', 3251,
  5. complement, negative strand, negative direction is SuccessablesCboxc--.bas, looking for 3'-TCATCA-5', 0,
  6. complement, negative strand, positive direction is SuccessablesCboxc-+.bas, looking for 3'-TCATCA-5', 1, 3'-TCATCA-5', 3251,
  7. complement, positive strand, negative direction is SuccessablesCboxc+-.bas, looking for 3'-TCATCA-5', 4, 3'-TCATCA-5', 2888, 3'-TCATCA-5', 2944, 3'-TCATCA-5', 3418, 3'-TCATCA-5', 3521,
  8. complement, positive strand, positive direction is SuccessablesCboxc++.bas, looking for 3'-TCATCA-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesCboxci--.bas, looking for 3'-ACTACT-5', 3, 3'-ACATCA-5', 2340, 3'-ACATCA-5', 2541, 3'-ACATCA-5', 4124,
  10. inverse complement, negative strand, positive direction is SuccessablesCboxci-+.bas, looking for 3'-ACTACT-5', 1, 3'-ACATCA-5', 4116,
  11. inverse complement, positive strand, negative direction is SuccessablesCboxci+-.bas, looking for 3'-ACTACT-5', 3, 3'-ACATCA-5', 2941, 3'-ACATCA-5', 3394, 3'-ACATCA-5', 3415,
  12. inverse complement, positive strand, positive direction is SuccessablesCboxci++.bas, looking for 3'-ACTACT-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesCboxi--.bas, looking for 3'-TGATGA-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesCboxi-+.bas, looking for 3'-TGATGA-5', 1, 3'-TGATGA-5', 2144,
  15. inverse, positive strand, negative direction, is SuccessablesCboxi+-.bas, looking for 3'-TGATGA-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesCboxi++.bas, looking for 3'-TGATGA-5', 0.

D box

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D box = 3'-AGTCTG-5'

For the Basic programs (starting with SuccessablesDbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDbox--.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 2947,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDbox-+.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 3923,
  3. positive strand in the negative direction is SuccessablesDbox+-.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 1355,
  4. positive strand in the positive direction is SuccessablesDbox++.bas, looking for 3'-AGTCTG-5', 0,
  5. complement, negative strand, negative direction is SuccessablesDboxc--.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 1355,
  6. complement, negative strand, positive direction is SuccessablesDboxc-+.bas, looking for 3'-TCAGAC-5', 0,
  7. complement, positive strand, negative direction is SuccessablesDboxc+-.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 2947,
  8. complement, positive strand, positive direction is SuccessablesDboxc++.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 3923,
  9. inverse complement, negative strand, negative direction is SuccessablesDboxci--.bas, looking for 3'-CAGACT-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesDboxci-+.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 1744, 3'-CAGACT-5', 2416,
  11. inverse complement, positive strand, negative direction is SuccessablesDboxci+-.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 15, 3'-CAGACT-5', 1616,
  12. inverse complement, positive strand, positive direction is SuccessablesDboxci++.bas, looking for 3'-CAGACT-5', 3, 3'-CAGACT-5', 2943, 3'-CAGACT-5', 3006, 3'-CAGACT-5', 3924,
  13. inverse, negative strand, negative direction, is SuccessablesDboxi--.bas, looking for 3'-GTCTGA-5', 2, 3'-GTCTGA-5', 15, 3'-GTCTGA-5', 1616,
  14. inverse, negative strand, positive direction, is SuccessablesDboxi-+.bas, looking for 3'-GTCTGA-5', 3, 3'-GTCTGA-5', 2943, 3'-GTCTGA-5', 3006, 3'-GTCTGA-5', 3924,
  15. inverse, positive strand, negative direction, is SuccessablesDboxi+-.bas, looking for 3'-GTCTGA-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesDboxi++.bas, looking for 3'-GTCTGA-5', 2, 3'-GTCTGA-5', 1744, 3'-GTCTGA-5', 2416.

CENP-B boxes

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Main resources: Gene transcriptions/Boxes/CENP-Bs and CENP-B boxes

The 17 nucleotide consensus sequence in the transcription direction on the template strand is 3'-TTTCGTTGGAAGCGGGA-5'.

For the Basic programs (starting with SuccessablesCENPB.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCENPB--.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCENPB-+.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  3. positive strand in the negative direction is SuccessablesCENPB+-.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  4. positive strand in the positive direction is SuccessablesCENPB++.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesCENPBc--.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesCENPBc-+.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesCENPBc+-.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  8. complement, positive strand, positive direction is SuccessablesCENPBc++.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesCENPBci--.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesCENPBci-+.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesCENPBci+-.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesCENPBci++.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesCENPB--.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesCENPB-+.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesCENPBi+-.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesCENPBi++.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0.

Increasing the number of nts from A1BG to ZNF497 from 958 to 4445 has yielded no CENP-B boxes.

CGCG boxes

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Main resources: Gene transcriptions/Boxes/CGCGs and CGCG boxes

"The minimum DNA-binding elements are 6-bp CGCG box, (A/C/G)CGCG(C/G/T)."[8]

For the Basic programs (starting with SuccessablesCGCG.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCGCG--.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 2, 3'-GCGCGT-5', 161, 3'-CCGCGC-5', 1761,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCGCG-+.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 8, 3'-GCGCGT-5', 543, 3'-CCGCGC-5', 681, 3'-GCGCGC-5', 683, 3'-ACGCGG-5', 871, 3'-ACGCGG-5', 971, 3'-CCGCGG-5', 1337, 3'-CCGCGG-5', 1437, 3'-CCGCGC-5', 1650,
  3. positive strand in the negative direction is SuccessablesCGCG+-.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 1, 3'-GCGCGG-5', 1762,
  4. positive strand in the positive direction is SuccessablesCGCG++.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 22, 3'-CCGCGC-5', 161, 3'-ACGCGG-5', 452, 3'-CCGCGC-5', 542, 3'-GCGCGC-5', 682, 3'-GCGCGT-5', 684, 3'-CCGCGT-5', 876, 3'-CCGCGT-5', 976, 3'-CCGCGT-5', 1046, 3'-ACGCGG-5', 1078, 3'-ACGCGG-5', 1162, 3'-CCGCGC-5', 1214, 3'-ACGCGG-5', 1246, 3'-CCGCGT-5', 1298, 3'-ACGCGT-5', 1314, 3'-ACGCGG-5', 1354, 3'-ACGCGG-5', 1398, 3'-ACGCGT-5', 1414, 3'-ACGCGG-5', 1454, 3'-ACGCGG-5', 1498, 3'-ACGCGT-5', 1523, 3'-CCGCGT-5', 1550, 3'-CCGCGG-5', 1769,
  5. complement, negative strand, negative direction is SuccessablesCGCGc--.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 1, 3'-CGCGCC-5', 1762,
  6. complement, negative strand, positive direction is SuccessablesCGCGc-+.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 22, 3'-GGCGCG-5', 161, 3'-TGCGCC-5', 452, 3'-GGCGCG-5', 542, 3'-CGCGCG-5', 682, 3'-CGCGCA-5', 684, 3'-GGCGCA-5', 876, 3'-GGCGCA-5', 976, 3'-GGCGCA-5', 1046, 3'-TGCGCC-5', 1078, 3'-TGCGCC-5', 1162, 3'-GGCGCG-5', 1214, 3'-TGCGCC-5', 1246, 3'-GGCGCA-5', 1298, 3'-TGCGCA-5', 1314, 3'-TGCGCC-5', 1354, 3'-TGCGCC-5', 1398, 3'-TGCGCA-5', 1414, 3'-TGCGCC-5', 1454, 3'-TGCGCC-5', 1498, 3'-TGCGCA-5', 1523, 3'-GGCGCA-5', 1550, 3'-GGCGCC-5', 1769,
  7. complement, positive strand, negative direction is SuccessablesCGCGc+-.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 2, 3'-CGCGCA-5', 161, 3'-GGCGCG-5', 1761,
  8. complement, positive strand, positive direction is SuccessablesCGCGc++.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 8, 3'-CGCGCA-5', 543, 3'-GGCGCG-5', 681, 3'-CGCGCG-5', 683, 3'-TGCGCC-5', 871, 3'-TGCGCC-5', 971, 3'-GGCGCC-5', 1337, 3'-GGCGCC-5', 1437, 3'-GGCGCG-5', 1650,
  9. inverse complement, negative strand, negative direction is SuccessablesCGCGci--.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 2, 3'-GCGCGT-5', 161, 3'-CCGCGC-5', 1761,
  10. inverse complement, negative strand, positive direction is SuccessablesCGCGci-+.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 8, 3'-GCGCGT-5', 543, 3'-CCGCGC-5', 681, 3'-GCGCGC-5', 683, 3'-ACGCGG-5', 871, 3'-ACGCGG-5', 971, 3'-CCGCGG-5', 1337, 3'-CCGCGG-5', 1437, 3'-CCGCGC-5', 1650,
  11. inverse complement, positive strand, negative direction is SuccessablesCGCGci+-.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 1, 3'-GCGCGG-5', 1762,
  12. inverse complement, positive strand, positive direction is SuccessablesCGCGci++.bas, looking for 3'-(A/C/G)CGCG(C/G/T)-5', 22, 3'-CCGCGC-5', 161, 3'-ACGCGG-5', 452, 3'-CCGCGC-5', 542, 3'-GCGCGC-5', 682, 3'-GCGCGT-5', 684, 3'-CCGCGT-5', 876, 3'-CCGCGT-5', 976, 3'-CCGCGT-5', 1046, 3'-ACGCGG-5', 1078, 3'-ACGCGG-5', 1162, 3'-CCGCGC-5', 1214, 3'-ACGCGG-5', 1246, 3'-CCGCGT-5', 1298, 3'-ACGCGT-5', 1314, 3'-ACGCGG-5', 1354, 3'-ACGCGG-5', 1398, 3'-ACGCGT-5', 1414, 3'-ACGCGG-5', 1454, 3'-ACGCGG-5', 1498, 3'-ACGCGT-5', 1523, 3'-CCGCGT-5', 1550, 3'-CCGCGG-5', 1769,
  13. inverse, negative strand, negative direction, is SuccessablesCGCGi--.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 1, 3'-CGCGCC-5', 1762,
  14. inverse, negative strand, positive direction, is SuccessablesCGCGi-+.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 22, 3'-GGCGCG-5', 161, 3'-TGCGCC-5', 452, 3'-GGCGCG-5', 542, 3'-CGCGCG-5', 682, 3'-CGCGCA-5', 684, 3'-GGCGCA-5', 876, 3'-GGCGCA-5', 976, 3'-GGCGCA-5', 1046, 3'-TGCGCC-5', 1078, 3'-TGCGCC-5', 1162, 3'-GGCGCG-5', 1214, 3'-TGCGCC-5', 1246, 3'-GGCGCA-5', 1298, 3'-TGCGCA-5', 1314, 3'-TGCGCC-5', 1354, 3'-TGCGCC-5', 1398, 3'-TGCGCA-5', 1414, 3'-TGCGCC-5', 1454, 3'-TGCGCC-5', 1498, 3'-TGCGCA-5', 1523, 3'-GGCGCA-5', 1550, 3'-GGCGCC-5', 1769,
  15. inverse, positive strand, negative direction, is SuccessablesCGCGi+-.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 2, 3'-CGCGCA-5', 161, 3'-GGCGCG-5', 1761,
  16. inverse, positive strand, positive direction, is SuccessablesCGCGi++.bas, looking for 3'-(C/G/T)GCGC(A/C/G)-5', 8, 3'-CGCGCA-5', 543, 3'-GGCGCG-5', 681, 3'-CGCGCG-5', 683, 3'-TGCGCC-5', 871, 3'-TGCGCC-5', 971, 3'-GGCGCC-5', 1337, 3'-GGCGCC-5', 1437, 3'-GGCGCG-5', 1650.

CRE boxes

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Main resources: Gene transcriptions/Boxes/CREs and CRE boxes

Consensus sequence is 3'-TGACGTCA-5'.

For the Basic programs (starting with SuccessablesCRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extension of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCRE--.bas, looking for 3'-TGACGTCA-5', 1, 3'-TGACGTCA-5', 4317,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCRE-+.bas, looking for 3'-TGACGTCA-5', 0,
  3. positive strand in the negative direction is SuccessablesCRE+-.bas, looking for 3'-TGACGTCA-5', 0,
  4. positive strand in the positive direction is SuccessablesCRE++.bas, looking for 3'-TGACGTCA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesCREc--.bas, looking for 3'-ACTGCAGT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesCREc-+.bas, looking for 3'-ACTGCAGT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesCREc+-.bas, looking for 3'-ACTGCAGT-5', 1, 3'-ACTGCAGT-5', 4317,
  8. complement, positive strand, positive direction is SuccessablesCREc++.bas, looking for 3'-ACTGCAGT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesCREci--.bas, looking for 3'-TGACGTCA-5', 1, 3'-TGACGTCA-5', 4317,
  10. inverse complement, negative strand, positive direction is SuccessablesCREci-+.bas, looking for 3'-TGACGTCA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesCREci+-.bas, looking for 3'-TGACGTCA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesCREci++.bas, looking for 3'-TGACGTCA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesCREi--.bas, looking for 3'-ACTGCAGT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesCREi-+.bas, looking for 3'-ACTGCAGT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesCREi+-.bas, looking for 3'-ACTGCAGT-5', 1, 3'-ACTGCAGT-5', 4317,
  16. inverse, positive strand, positive direction, is SuccessablesCREi++.bas, looking for 3'-ACTGCAGT-5', 0.

DREB boxes

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Main resources: Gene transcriptions/Boxes/DREBs and DREB boxes

Consensus sequence for the dehydration-responsive element-binding (DREB) box is 3'-TACCGACAT-5'.

For the Basic programs (starting with SuccessablesDREB.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDREB--.bas, looking for 3'-TACCGACAT-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDREB-+.bas, looking for 3'-TACCGACAT-5', 0,
  3. positive strand in the negative direction is SuccessablesDREB+-.bas, looking for 3'-TACCGACAT-5', 0,
  4. positive strand in the positive direction is SuccessablesDREB++.bas, looking for 3'-TACCGACAT-5', 0,
  5. complement, negative strand, negative direction is SuccessablesDREBc--.bas, looking for 3'-ATGGCTGTA-5', 0,
  6. complement, negative strand, positive direction is SuccessablesDREBc-+.bas, looking for 3'-ATGGCTGTA-5', 0,
  7. complement, positive strand, negative direction is SuccessablesDREBc+-.bas, looking for 3'-ATGGCTGTA-5', 0,
  8. complement, positive strand, positive direction is SuccessablesDREBc++.bas, looking for 3'-ATGGCTGTA-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesDREBci--.bas, looking for 3'-ATGTCGGTA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesDREBci-+.bas, looking for 3'-ATGTCGGTA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesDREBci+-.bas, looking for 3'-ATGTCGGTA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesDREBci++.bas, looking for 3'-ATGTCGGTA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesDREBi--.bas, looking for 3'-TACAGCCAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesDREBi-+.bas, looking for 3'-TACAGCCAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesDREBi+-.bas, looking for 3'-TACAGCCAT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesDREBi++.bas, looking for 3'-TACAGCCAT-5', 0.

Increasing the number of nts from A1BG to ZNF497 from 958 to 4445 has yielded no DREB boxes.

E2 boxes

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Main resources: Gene transcriptions/Boxes/E2s and E2 boxes

"The most dramatic impact on immunoglobulin gene enhancer activity was observed upon mutation of sites that contain an E2-box motif (G/ACAGNTGN)."[9]

For the Basic programs (starting with SuccessablesE2box.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesE2box--.bas, looking for 3'-(G/A)CAG(A/C/G/T)TG(A/C/G/T)-5', 5, 3'-ACAGATGT-5', 482, 3'-ACAGATGT-5', 1225, 3'-GCAGTTGG-5', 1514, 3'-ACAGATGT-5', 2989, 3'-ACAGATGT-5', 4213,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesE2box-+.bas, looking for 3'-(G/A)CAG(A/C/G/T)TG(A/C/G/T)-5', 1, 3'-GCAGATGA-5', 37,
  3. positive strand in the negative direction is SuccessablesE2box+-.bas, looking for 3'-(G/A)CAG(A/C/G/T)TG(A/C/G/T)-5', 2, 3'-GCAGGTGG-5', 2571, 3'-ACAGATGA-5', 3920,
  4. positive strand in the positive direction is SuccessablesE2box++.bas, looking for 3'-(G/A)CAG(A/C/G/T)TG(A/C/G/T)-5', 0,
  5. complement, negative strand, negative direction is SuccessablesE2boxc--.bas, looking for 3'-(C/T)GTC(A/C/G/T)AC(A/C/G/T)-5', 2, 3'-CGTCCACC-5', 2571, 3'-TGTCTACT-5', 3920,
  6. complement, negative strand, positive direction is SuccessablesE2boxc-+.bas, looking for 3'-(C/T)GTC(A/C/G/T)AC(A/C/G/T)-5', 0,
  7. complement, positive strand, negative direction is SuccessablesE2boxc+-.bas, looking for 3'-(C/T)GTC(A/C/G/T)AC(A/C/G/T)-5', 5, 3'-TGTCTACA-5', 482, 3'-TGTCTACA-5', 1225, 3'-CGTCAACC-5', 1514, 3'-TGTCTACA-5', 2989, 3'-TGTCTACA-5', 4213,
  8. complement, positive strand, positive direction is SuccessablesE2boxc++.bas, looking for 3'-(C/T)GTC(A/C/G/T)AC(A/C/G/T)-5', 1, 3'-CGTCTACT-5', 37,
  9. inverse complement, negative strand, negative direction is SuccessablesE2boxci--.bas, looking for 3'-(A/C/G/T)CA(A/C/G/T)CTG(C/T)-5', 1, 3'-CCACCTGT-5', 2117,
  10. inverse complement, negative strand, positive direction is SuccessablesE2boxci-+.bas, looking for 3'-(A/C/G/T)CA(A/C/G/T)CTG(C/T)-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesE2boxci+-.bas, looking for 3'-(A/C/G/T)CA(A/C/G/T)CTG(C/T)-5', 4, 3'-CCACCTGT-5', 394, 3'-ACACCTGT-5', 1131, 3'-GCAACTGC-5', 3851, 3'-ACACCTGT-5', 3970,
  12. inverse complement, positive strand, positive direction is SuccessablesE2boxci++.bas, looking for 3'-(A/C/G/T)CA(A/C/G/T)CTG(C/T)-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesE2boxi--.bas, looking for 3'-(A/C/G/T)GT(A/C/G/T)GAC(G/A)-5', 4, 3'-GGTGGACA-5', 394, 3'-TGTGGACA-5', 1131, 3'-CGTTGACG-5', 3851, 3'-TGTGGACA-5', 3970,
  14. inverse, negative strand, positive direction, is SuccessablesE2boxi-+.bas, looking for 3'-(A/C/G/T)GT(A/C/G/T)GAC(G/A)-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesE2box+-.bas, looking for 3'-(A/C/G/T)GT(A/C/G/T)GAC(G/A)-5', 1, 3'-GGTGGACA-5', 2117,
  16. inverse, positive strand, positive direction, is SuccessablesE2boxi++.bas, looking for 3'-(A/C/G/T)GT(A/C/G/T)GAC(G/A)-5', 0.

EIF4E basal elements

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Main resources: Gene transcriptions/Elements/EIF4E basals and EIF4E basal elements

The EIF4E basal element, also eIF4E, (4EBE) is a basal promoter element for the eukaryotic translation initiation factor 4E. "Interactions between 4EBE and upstream activator sites are position, distance, and sequence dependent."[10]

The consensus sequence is 3'-TTACCCCCCCTT-5' in the direction of transcription.[10]

For the Basic programs (starting with Successables4EBE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction is Successables4EBE--.bas, looking for 3'-TTACCCCCCCTT-5', 0,
  2. negative strand in the positive direction is Successables4EBE-+.bas, looking for 3'-TTACCCCCCCTT-5', 0,
  3. positive strand in the negative direction is Successables4EBE+-.bas, looking for 3'-TTACCCCCCCTT-5', 0,
  4. positive strand in the positive direction is Successables4EBE++.bas, looking for 3'-TTACCCCCCCTT-5', 0,
  5. complement, negative strand, negative direction is Successables4EBEc--.bas, looking for 3'-AATGGGGGGGAA-5', 0,
  6. complement, negative strand, positive direction is Successables4EBEc-+.bas, looking for 3'-AATGGGGGGGAA-5', 0,
  7. complement, positive strand, negative direction is Successables4EBEc+-.bas, looking for 3'-AATGGGGGGGAA-5', 0,
  8. complement, positive strand, negative direction is Successables4EBEc++.bas, looking for 3'-AATGGGGGGGAA-5', 0,
  9. inverse complement, negative strand, negative direction is Successables4EBEci--.bas, looking for 3'-AAGGGGGGGTAA-5', 0,
  10. inverse complement, negative strand, positive direction is Successables4EBEci-+.bas, looking for 3'-AAGGGGGGGTAA-5', 0,
  11. inverse complement, positive strand, negative direction is Successables4EBEci+-.bas, looking for 3'-AAGGGGGGGTAA-5', 0,
  12. inverse complement, positive strand, positive direction is Successables4EBEci++.bas, looking for 3'-AAGGGGGGGTAA-5', 0,
  13. inverse, negative strand, negative direction, is Successables4EBEi--.bas, looking for 3'-TTCCCCCCCATT-5', 0,
  14. inverse, negative strand, positive direction, is Successables4EBEi--.bas, looking for 3'-TTCCCCCCCATT-5', 0,
  15. inverse, positive strand, negative direction, is Successables4EBEi+-.bas, looking for 3'-TTCCCCCCCATT-5', 0,
  16. inverse, positive strand, positive direction, is Successables4EBEi++.bas, looking for 3'-TTCCCCCCCATT-5', 0.

GAREs

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Main resources: Gene transcriptions/GAREs and GAREs

"Although this GARC [GA responsive complex] may not always be tripartite, most often it includes three sequence motifs, the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994)."[11]

For the Basic programs (starting with SuccessablesGARE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGARE--.bas, looking for 3'-TAACAAA-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGARE-+.bas, looking for 3'-TAACAAA-5', 0,
  3. positive strand in the negative direction is SuccessablesGARE+-.bas, looking for 3'-TAACAAA-5', 0,
  4. positive strand in the positive direction is SuccessablesGARE++.bas, looking for 3'-TAACAAA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesGAREc--.bas, looking for 3'-ATTGTTT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesGAREc-+.bas, looking for 3'-ATTGTTT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesGAREc+-.bas, looking for 3'-ATTGTTT-5', 0,
  8. complement, positive strand, positive direction is SuccessablesGAREc++.bas, looking for 3'-ATTGTTT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesGAREci--.bas, looking for 3'-TTTGTTA-5', 1, 3'-TTTGTTA-5', 230,
  10. inverse complement, negative strand, positive direction is SuccessablesGAREci-+.bas, looking for 3'-TTTGTTA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesGAREci+-.bas, looking for 3'-TTTGTTA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesGAREci++.bas, looking for 3'-TTTGTTA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGAREi--.bas, looking for 3'-AAACAAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesGAREi-+.bas, looking for 3'-AAACAAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGAREi+-.bas, looking for 3'-AAACAAT-5', 1, 3'-AAACAAT-5', 230,
  16. inverse, positive strand, positive direction, is SuccessablesGAREi++.bas, looking for 3'-AAACAAT-5', 0.

G boxes

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Main resources: Gene transcriptions/Boxes/Gs and G boxes

The "perfect palindrome 5'-GCCACGTGGC-3' which is also known as the G-box motif."[12]

For the Basic programs (starting with SuccessablesGbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGbox--.bas, looking for 3'-GCCACGTGGC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGbox-+.bas, looking for 3'-GCCACGTGGC-5', 0,
  3. positive strand in the negative direction is SuccessablesGbox+-.bas, looking for 3'-GCCACGTGGC-5', 0,
  4. positive strand in the positive direction is SuccessablesGbox++.bas, looking for 3'-GCCACGTGGC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesGboxc--.bas, looking for 3'-CGGTGCACCG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesGboxc-+.bas, looking for 3'-CGGTGCACCG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesGboxc+-.bas, looking for 3'-CGGTGCACCG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesGboxc++.bas, looking for 3'-CGGTGCACCG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesGboxci--.bas, looking for 3'-GCCACGTGGC-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesGboxci-+.bas, looking for 3'-GCCACGTGGC-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesGboxci+-.bas, looking for 3'-GCCACGTGGC-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesGboxci++.bas, looking for 3'-GCCACGTGGC-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGboxi--.bas, looking for 3'-CGGTGCACCG-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesGboxi-+.bas, looking for 3'-CGGTGCACCG-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGboxi+-.bas, looking for 3'-CGGTGCACCG-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesGboxi++.bas, looking for 3'-CGGTGCACCG-5', 0.

GC boxes

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Main resources: Gene transcriptions/Boxes/GC and GC boxes

"A GC box sequence, one of the most common regulatory DNA elements of eukaryotic genes, is recognized by the Spl transcription factor; its consensus sequence is represented as 5'-G/T G/A GGCG G/T G/A G/A C/T-3' [or 5′-KRGGCGKRRY-3′] (Briggs et al., 1986)."[13]

For the Basic programs (starting with SuccessablesGC.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction is SuccessablesGC--.bas, looking for 3'-G/T G/A GGCG G/T G/A G/A C/T-5', 0,
  2. negative strand in the positive direction is SuccessablesGC-+.bas, looking for 3'-G/T G/A GGCG G/T G/A G/A C/T-5', 0,
  3. positive strand in the negative direction is SuccessablesGC+-.bas, looking for 3'-G/T G/A GGCG G/T G/A G/A C/T-5', 2, 3'-TGGGCGTGGT-5', 1898, 3'-TGGGCGTGGT-5', 3048 ,
  4. positive strand in the positive direction is SuccessablesGC++.bas, looking for 3'-G/T G/A GGCG G/T G/A G/A C/T-5', 0,
  5. complement, negative strand, negative direction is SuccessablesGCc--.bas, looking for 3'-A/C C/T CCGC A/C C/T C/T A/G-5', 2, 3'-ACCCGCACCA-5', 1898, 3'-ACCCGCACCA-5', 3048,
  6. complement, negative strand, positive direction is SuccessablesGCc-+.bas, looking for 3'-A/C C/T CCGC A/C C/T C/T A/G-5', 0,
  7. complement, positive strand, negative direction is SuccessablesGCc+-.bas, looking for 3'-A/C C/T CCGC A/C C/T C/T A/G-5', 0,
  8. complement, positive strand, negative direction is SuccessablesGCc++.bas, looking for 3'-A/C C/T CCGC A/C C/T C/T A/G-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesGCci--.bas, looking for 3'-A/G C/T C/T A/C CGCC C/T A/C-5', 1, 3'-ACTCCGCCCA-5', 3092,
  10. inverse complement, negative strand, positive direction is SuccessablesGCci-+.bas, looking for 3'-A/G C/T C/T A/C CGCC C/T A/C-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesGCci+-.bas, looking for 3'-A/G C/T C/T A/C CGCC C/T A/C-5', 1, 3'-GCTCCGCCTC-5', 1505,
  12. inverse complement, positive strand, positive direction is SuccessablesGCci++.bas, looking for 3'-A/G C/T C/T A/C CGCC C/T A/C-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGCi--.bas, looking for 3'-C/T G/A G/A G/T GCGG G/A G/T-5', 1, 3'-CGAGGCGGAG-5', 1505,
  14. inverse, negative strand, positive direction, is SuccessablesGCi-+.bas, looking for 3'-C/T G/A G/A G/T GCGG G/A G/T-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGCi+-.bas, looking for 3'-C/T G/A G/A G/T GCGG G/A G/T-5', 1, 3'-TGAGGCGGGT-5', 3092,
  16. inverse, positive strand, positive direction, is SuccessablesGCi++.bas, looking for 3'-C/T G/A G/A G/T GCGG G/A G/T-5', 0.

GCC boxes

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Main resources: Gene transcriptions/Boxes/GCC and GCC boxes

The "EREBP-like (ethylene responsive element binding protein) proteins [bind] the GCC box (consensus sequence AGCCGCC) (Ohme-Takagi and Shinshi 1995; Sakuma et al. 2002)."[14]

The GCC box is the same as the AGC box.

For the Basic programs (starting with SuccessablesGCC.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGCC--.bas, looking for 3'-AGCCGCC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGCC-+.bas, looking for 3'-AGCCGCC-5', 0,
  3. positive strand in the negative direction is SuccessablesGCC+-.bas, looking for 3'-AGCCGCC-5', 0,
  4. positive strand in the positive direction is SuccessablesGCC++.bas, looking for 3'-AGCCGCC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesGCCc--.bas, looking for 3'-TCGGCGG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesGCCc-+.bas, looking for 3'-TCGGCGG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesGCCc+-.bas, looking for 3'-TCGGCGG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesGCCc++.bas, looking for 3'-TCGGCGG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesGCCci--.bas, looking for 3'-GGCGGCT-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesGCCci-+.bas, looking for 3'-GGCGGCT-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesGCCci+-.bas, looking for 3'-GGCGGCT-5', 1, 3'-GGCGGCT-5', 1754,
  12. inverse complement, positive strand, positive direction is SuccessablesGCCci++.bas, looking for 3'-GGCGGCT-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGCCi--.bas, looking for 3'-CCGCCGA-5', 1, 3'-CCGCCGA-5', 1754,
  14. inverse, negative strand, positive direction, is SuccessablesGCCi-+.bas, looking for 3'-CCGCCGA-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGCCi+-.bas, looking for 3'-CCGCCGA-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesGCCi++.bas, looking for 3'-CCGCCGA-5', 0.

GLM boxes

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Main resources: Gene transcriptions/Boxes/GLMs and GLM boxes

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995). The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."[15]

For the Basic programs (starting with SuccessablesGLM.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGLM--.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGLM-+.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
  3. positive strand in the negative direction is SuccessablesGLM+-.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
  4. positive strand in the positive direction is SuccessablesGLM++.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
  5. complement, negative strand, negative direction is SuccessablesGLMc--.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
  6. complement, negative strand, positive direction is SuccessablesGLMc-+.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
  7. complement, positive strand, negative direction is SuccessablesGLMc+-.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
  8. complement, positive strand, positive direction is SuccessablesGLMc++.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesGLMci--.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesGLMci-+.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesGLMci+-.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesGLMci++.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGLMi--.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesGLMi-+.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGLMi+-.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesGLMi++.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0.

H boxes

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Main resources: Gene transcriptions/Boxes/H and ACA and H and ACA boxes

An H box has a consensus sequence of 3'-ACACCA-5'.[16]

For the Basic programs (starting with SuccessablesHACA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesHACA--.bas, looking for 3'-ACACCA-5', 4, 3'-ACACCA-5', 788, 3'-ACACCA-5', 2659, 3'-ACACCA-5', 3187, 3'-ACACCA-5', 3811,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHACA-+.bas, looking for 3'-ACACCA-5', 1, 3'-ACACCA-5', 386,
  3. positive strand in the negative direction is SuccessablesHACA+-.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 883, 3'-ACACCA-5', 2419,
  4. positive strand in the positive direction is SuccessablesHACA++.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 204, 3'-ACACCA-5', 528,
  5. complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 883, 3'-TGTGGT-5', 2419,
  6. complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 204, 3'-TGTGGT-5', 528,
  7. complement, positive strand, negative direction is SuccessablesHACAc+-.bas, looking for 3'-TGTGGT-5', 4, 3'-TGTGGT-5', 788, 3'-TGTGGT-5', 2659, 3'-TGTGGT-5', 3187, 3'-TGTGGT-5', 3811,
  8. complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 3'-TGTGGT-5', 1, 3'-TGTGGT-5', 386,
  9. inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 3764,
  10. inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 3'-TGGTGT-5', 2, 3'-TGGTGT-5', 511, 3'-TGGTGT-5', 530,
  11. inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 3'-TGGTGT-5', 3, 3'-TGGTGT-5', 608, 3'-TGGTGT-5', 793, 3'-TGGTGT-5', 1477,
  12. inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 420,
  13. inverse, negative strand, negative direction, is SuccessablesHACAi--.bas, looking for 3'-ACCACA-5', 3, 3'-ACCACA-5', 608, 3'-ACCACA-5', 793, 3'-ACCACA-5', 1477,
  14. inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 420,
  15. inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 3764,
  16. inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 3'-ACCACA-5', 2, 3'-ACCACA-5', 511, 3'-ACCACA-5', 530.

HMG boxes

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Main resources: Gene transcriptions/Boxes/HMGs and HMG boxes

"Most HMG box proteins contain two or more HMG boxes and appear to bind DNA in a relatively sequence-aspecific manner (5, 13, 15, 16 and references therein). [...] they all appear to bind to the minor groove of the A/T A/T C A A A G-motif (10, 14, 18-20)."[17]

For the Basic programs (starting with SuccessablesHMG.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesHMG--.bas, looking for 3'-(A/T)(A/T)CAAAG-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHMG-+.bas, looking for 3'-(A/T)(A/T)CAAAG-5', 0,
  3. positive strand in the negative direction is SuccessablesHMG+-.bas, looking for 3'-(A/T)(A/T)CAAAG-5', 1, 3'-ATCAAAG-5', 2891,
  4. positive strand in the positive direction is SuccessablesHMG++.bas, looking for 3'-(A/T)(A/T)CAAAG-5', 0,
  5. complement, negative strand, negative direction is SuccessablesHMGc--.bas, looking for 3'-(A/T)(A/T)GTTTC-5', 1, 3'-TAGTTTC-5', 2891,
  6. complement, negative strand, positive direction is SuccessablesHMGc-+.bas, looking for 3'-(A/T)(A/T)GTTTC-5', 0,
  7. complement, positive strand, negative direction is SuccessablesHMGc+-.bas, looking for 3'-(A/T)(A/T)GTTTC-5', 0,
  8. complement, positive strand, positive direction is SuccessablesHMGc++.bas, looking for 3'-(A/T)(A/T)GTTTC-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesHMGci--.bas, looking for 3'-CTTTG(A/T)(A/T)-5', 2, 3'-CTTTGTT-5', 229, 3'-CTTTGTT-5', 1585,
  10. inverse complement, negative strand, positive direction is SuccessablesHMGci-+.bas, looking for 3'-CTTTG(A/T)(A/T)-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesHMGci+-.bas, looking for 3'-CTTTG(A/T)(A/T)-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesHMGci++.bas, looking for 3'-CTTTG(A/T)(A/T)-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesHMGi--.bas, looking for 3'-GAAAC(A/T)(A/T)-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesHMGi-+.bas, looking for 3'-GAAAC(A/T)(A/T)-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesHMGi+-.bas, looking for 3'-GAAAC(A/T)(A/T)-5', 2, 3'-GAAACAA-5', 229, 3'-GAAACAA-5', 1585,
  16. inverse, positive strand, positive direction, is SuccessablesHMGi++.bas, looking for 3'-GAAAC(A/T)(A/T)-5', 0.

M35 boxes

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Main resources: Gene transcriptions/Boxes/M35s and M35 boxes

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated(1-5). [One of these domains is] the -35 sequence [M35 box] (5'-T-T-G-A-C-A)".[18]

For the Basic programs (starting with SuccessablesM35.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesM35--.bas, looking for 3'-TTGACA-5', 2, 3'-TTGACA-5', 477, 3'-TTGACA-5', 4399,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesM35-+.bas, looking for 3'-TTGACA-5', 0,
  3. positive strand in the negative direction is SuccessablesM35+-.bas, looking for 3'-TTGACA-5', 0,
  4. positive strand in the positive direction is SuccessablesM35++.bas, looking for 3'-TTGACA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesM35c--.bas, looking for 3'-AACTGT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesM35c-+.bas, looking for 3'-AACTGT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesM35c+-.bas, looking for 3'-AACTGT-5', 2, 3'-AACTGT-5', 477, 3'-AACTGT-5', 4399,
  8. complement, positive strand, positive direction is SuccessablesM35c++.bas, looking for 3'-AACTGT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesM35ci--.bas, looking for 3'-TGTCAA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesM35ci-+.bas, looking for 3'-TGTCAA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesM35ci+-.bas, looking for 3'-TGTCAA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesM35ci++.bas, looking for 3'-TGTCAA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesM35i--.bas, looking for 3'-ACAGTT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesM35i-+.bas, looking for 3'-ACAGTT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesM35i+-.bas, looking for 3'-ACAGTT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesM35i++.bas, looking for 3'-ACAGTT-5', 0.

P boxes

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Main resources: Gene transcriptions/Boxes/V and P and V and P boxes

"As VRI [target gene: vrille (VRI)] accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[19]

For the Basic programs (starting with SuccessablesPbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPbox--.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 84, 3'-ATTTT-5', 66, 3'-GTTTC-5', 93, 3'-GTAAT-5', 153, 3'-GTTTT-5', 164, 3'-GTAAT-5', 173, 3'-ATATT-5', 181, 3'-ATTTT-5', 183, 3'-ATATT-5', 220, 3'-ATTTT-5', 222, 3'-ATAAT-5', 236, 3'-ATTAT-5', 249, 3'-GTTTT-5', 257, 3'-GTATT-5', 269, 3'-ATTAT-5', 271, 3'-GTATC-5', 468, 3'-GTTTT-5', 485, 3'-ATTAT-5', 602, 3'-ATTTT-5', 629, 3'-GTTTT-5', 637, 3'-ATTTT-5', 763, 3'-GTTTT-5', 771, 3'-GTAAC-5', 886, 3'-GTTTT-5', 926, 3'-GTTTT-5', 1092, 3'-GTTTT-5', 1228, 3'-GTAAC-5', 1343, 3'-GTTAT-5', 1362, 3'-GTTTT-5', 1371, 3'-GTTTT-5', 1384, 3'-GTTTT-5', 1394, 3'-ATTTC-5', 1548, 3'-GTTTT-5', 1561, 3'-GTTTC-5', 1638, 3'-ATTAT-5', 1708, 3'-ATTTT-5', 1737, 3'-ATTTT-5', 1872, 3'-GTTTT-5', 1880, 3'-GTTTT-5', 2036, 3'-ATTTC-5', 2174, 3'-GTTTT-5', 2182, 3'-ATTTT-5', 2299, 3'-GTTTT-5', 2307, 3'-GTTTT-5', 2476, 3'-GTTTT-5', 2490, 3'-GTTAT-5', 2497, 3'-GTTTT-5', 2644, 3'-GTTTT-5', 2795, 3'-GTTAT-5', 2849, 3'-ATTTC-5', 2857, 3'-GTTTT-5', 2866, 3'-ATATT-5', 2873, 3'-GTTTC-5', 2891, 3'-ATATC-5', 2902, 3'-GTAAT-5', 2951, 3'-ATAAT-5', 2977, 3'-ATAAT-5', 2998, 3'-ATTTT-5', 3010, 3'-ATTTT-5', 3024, 3'-ATTTT-5', 3163, 3'-GTATT-5', 3169, 3'-ATTTT-5', 3171, 3'-GTAAC-5', 3285, 3'-GTTTT-5', 3313, 3'-GTTTT-5', 3326, 3'-ATTTT-5', 3353, 3'-GTATC-5', 3421, 3'-GTAAT-5', 3436, 3'-ATTTT-5', 3439, 3'-GTATC-5', 3446, 3'-ATAAT-5', 3454, 3'-ATAAT-5', 3468, 3'-ATAAC-5', 3528, 3'-ATTAT-5', 3538, 3'-ATTAC-5', 3658, 3'-GTTTT-5', 3767, 3'-GTATC-5', 4046, 3'-GTTTT-5', 4066, 3'-ATTAT-5', 4077, 3'-GTTTT-5', 4216, 3'-ATTAT-5', 4223, 3'-GTTTT-5', 4310, 3'-GTTTT-5', 4376, 3'-GTTTC-5', 4504, 3'-ATAAT-5', 4538,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPbox-+.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 6, 3'-GTAAC-5', 293, 3'-GTTTT-5', 670, 3'-ATTTT-5', 681, 3'-ATTAT-5', 719, 3'-ATTAT-5', 726, 3'-ATAAT-5', 729,
  3. positive strand in the negative direction is SuccessablesPbox+-.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 40, 3'-ATTTC-5', 22, 3'-ATTTT-5', 190, 3'-GTTTT-5', 215, 3'-GTAAT-5', 248, 3'-ATAAT-5', 270, 3'-GTAAT-5', 397, 3'-GTAAT-5', 534, 3'-GTAAC-5', 613, 3'-GTAAT-5', 670, 3'-GTAAT-5', 804, 3'-GTAAT-5', 1134, 3'-GTAAT-5', 1261, 3'-ATTAC-5', 1296, 3'-ATTTC-5', 1380, 3'-ATATC-5', 1528, 3'-ATATT-5', 1601, 3'-ATTTC-5', 1603, 3'-GTAAT-5', 1707, 3'-ATTAT-5', 1724, 3'-ATTTT-5', 1727, 3'-GTAAT-5', 1779, 3'-GTAAT-5', 1914, 3'-GTAAT-5', 2088, 3'-GTAAT-5', 2675, 3'-ATATT-5', 2851, 3'-ATTTT-5', 2853, 3'-ATTTC-5', 2884, 3'-GTAAT-5', 3064, 3'-GTTTT-5', 3349, 3'-ATATT-5', 3453, 3'-ATATT-5', 3467, 3'-ATTAC-5', 3469, 3'-ATAAT-5', 3537, 3'-ATAAT-5', 3657, 3'-ATTTC-5', 3688, 3'-GTAAT-5', 3973, 3'-ATAAT-5', 4076, 3'-ATAAT-5', 4222, 3'-ATAAT-5', 4225, 3'-ATTTT-5', 4511,
  4. positive strand in the positive direction is SuccessablesPbox++.bas, looking for 3'-(A/G)T(A/T)(A/T)(T/C)-5', 5, 3'-ATATC-5', 261, 3'-ATAAT-5', 704, 3'-ATAAC-5', 721, 3'-ATATT-5', 728, 3'-GTAAC-5', 871,
  5. complement, negative strand, negative direction is SuccessablesPboxc--.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 40, 3'-TAAAG-5', 22, 3'-TAAAA-5', 190, 3'-CAAAA-5', 215, 3'-CATTA-5', 248, 3'-TATTA-5', 270, 3'-CATTA-5', 397, 3'-CATTA-5', 534, 3'-CATTG-5', 613, 3'-CATTA-5', 670, 3'-CATTA-5', 804, 3'-CATTA-5', 1134, 3'-CATTA-5', 1261, 3'-TAATG-5', 1296, 3'-TAAAG-5', 1380, 3'-TATAG-5', 1528, 3'-TATAA-5', 1601, 3'-TAAAG-5', 1603, 3'-CATTA-5', 1707, 3'-TAATA-5', 1724, 3'-TAAAA-5', 1727, 3'-CATTA-5', 1779, 3'-CATTA-5', 1914, 3'-CATTA-5', 2088, 3'-CATTA-5', 2675, 3'-TATAA-5', 2851, 3'-TAAAA-5', 2853, 3'-TAAAG-5', 2884, 3'-CATTA-5', 3064, 3'-CAAAA-5', 3349, 3'-TATAA-5', 3453, 3'-TATAA-5', 3467, 3'-TAATG-5', 3469, 3'-TATTA-5', 3537, 3'-TATTA-5', 3657, 3'-TAAAG-5', 3688, 3'-CATTA-5', 3973, 3'-TATTA-5', 4076, 3'-TATTA-5', 4222, 3'-TATTA-5', 4225, 3'-TAAAA-5', 4511,
  6. complement, negative strand, positive direction is SuccessablesPboxc-+.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 5, 3'-TATAG-5', 261, 3'-TATTA-5', 704, 3'-TATTG-5', 721, 3'-TATAA-5', 728, 3'-CATTG-5', 871,
  7. complement, positive strand, negative direction is SuccessablesPboxc+-.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 84, 3'-TAAAA-5', 66, 3'-CAAAG-5', 93, 3'-CATTA-5', 153, 3'-CAAAA-5', 164, 3'-CATTA-5', 173, 3'-TATAA-5', 181, 3'-TAAAA-5', 183, 3'-TATAA-5', 220, 3'-TAAAA-5', 222, 3'-TATTA-5', 236, 3'-TAATA-5', 249, 3'-CAAAA-5', 257, 3'-CATAA-5', 269, 3'-TAATA-5', 271, 3'-CATAG-5', 468, 3'-CAAAA-5', 485, 3'-TAATA-5', 602, 3'-TAAAA-5', 629, 3'-CAAAA-5', 637, 3'-TAAAA-5', 763, 3'-CAAAA-5', 771, 3'-CATTG-5', 886, 3'-CAAAA-5', 926, 3'-CAAAA-5', 1092, 3'-CAAAA-5', 1228, 3'-CATTG-5', 1343, 3'-CAATA-5', 1362, 3'-CAAAA-5', 1371, 3'-CAAAA-5', 1384, 3'-CAAAA-5', 1394, 3'-TAAAG-5', 1548, 3'-CAAAA-5', 1561, 3'-CAAAG-5', 1638, 3'-TAATA-5', 1708, 3'-TAAAA-5', 1737, 3'-TAAAA-5', 1872, 3'-CAAAA-5', 1880, 3'-CAAAA-5', 2036, 3'-TAAAG-5', 2174, 3'-CAAAA-5', 2182, 3'-TAAAA-5', 2299, 3'-CAAAA-5', 2307, 3'-CAAAA-5', 2476, 3'-CAAAA-5', 2490, 3'-CAATA-5', 2497, 3'-CAAAA-5', 2644, 3'-CAAAA-5', 2795, 3'-CAATA-5', 2849, 3'-TAAAG-5', 2857, 3'-CAAAA-5', 2866, 3'-TATAA-5', 2873, 3'-CAAAG-5', 2891, 3'-TATAG-5', 2902, 3'-CATTA-5', 2951, 3'-TATTA-5', 2977, 3'-TATTA-5', 2998, 3'-TAAAA-5', 3010, 3'-TAAAA-5', 3024, 3'-TAAAA-5', 3163, 3'-CATAA-5', 3169, 3'-TAAAA-5', 3171, 3'-CATTG-5', 3285, 3'-CAAAA-5', 3313, 3'-CAAAA-5', 3326, 3'-TAAAA-5', 3353, 3'-CATAG-5', 3421, 3'-CATTA-5', 3436, 3'-TAAAA-5', 3439, 3'-CATAG-5', 3446, 3'-TATTA-5', 3454, 3'-TATTA-5', 3468, 3'-TATTG-5', 3528, 3'-TAATA-5', 3538, 3'-TAATG-5', 3658, 3'-CAAAA-5', 3767, 3'-CATAG-5', 4046, 3'-CAAAA-5', 4066, 3'-TAATA-5', 4077, 3'-CAAAA-5', 4216, 3'-TAATA-5', 4223, 3'-CAAAA-5', 4310, 3'-CAAAA-5', 4376, 3'-CAAAG-5', 4504, 3'-TATTA-5', 4538,
  8. complement, positive strand, positive direction is SuccessablesPboxc++.bas, looking for 3'-(C/T)A(A/T)(A/T)(A/G)-5', 6, 3'-CATTG-5', 293, 3'-CAAAA-5', 670, 3'-TAAAA-5', 681, 3'-TAATA-5', 719, 3'-TAATA-5', 726, 3'-TATTA-5', 729,
  9. inverse complement, negative strand, negative direction is SuccessablesPboxci--.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 54, 3'-AAAAC-5', 28, 3'-GAAAT-5', 48, 3'-GTAAT-5', 153, 3'-GTAAT-5', 173, 3'-AAAAT-5', 191, 3'-GATAC-5', 211, 3'-AAAAT-5', 217, 3'-AATAT-5', 219, 3'-ATAAT-5', 236, 3'-ATTAT-5', 249, 3'-ATTAT-5', 271, 3'-GAAAT-5', 348, 3'-AATAC-5', 350, 3'-GAAAC-5', 409, 3'-GAAAC-5', 546, 3'-ATTAT-5', 602, 3'-GAAAC-5', 682, 3'-GTAAC-5', 886, 3'-GAAAC-5', 1146, 3'-GTAAC-5', 1343, 3'-GTTAT-5', 1362, 3'-AAAAC-5', 1433, 3'-GATAT-5', 1526, 3'-GAAAC-5', 1688, 3'-ATTAT-5', 1708, 3'-AAAAT-5', 1728, 3'-GAAAT-5', 1734, 3'-GAAAC-5', 1791, 3'-GAAAC-5', 2100, 3'-GAAAC-5', 2217, 3'-GTTAT-5', 2497, 3'-GAAAC-5', 2553, 3'-GTTAT-5', 2849, 3'-AAAAT-5', 2854, 3'-GATAT-5', 2899, 3'-GTAAT-5', 2951, 3'-ATAAT-5', 2977, 3'-ATAAT-5', 2998, 3'-AAAAT-5', 3021, 3'-GAAAC-5', 3076, 3'-GTAAC-5', 3285, 3'-AAAAT-5', 3350, 3'-GTAAT-5', 3436, 3'-ATAAT-5', 3454, 3'-ATAAT-5', 3468, 3'-ATAAC-5', 3528, 3'-ATTAT-5', 3538, 3'-ATTAC-5', 3658, 3'-GAAAC-5', 3985, 3'-ATTAT-5', 4077, 3'-ATTAT-5', 4223, 3'-GAAAC-5', 4462, 3'-AAAAT-5', 4512, 3'-ATAAT-5', 4538,
  10. inverse complement, negative strand, positive direction is SuccessablesPboxci-+.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 6, 3'-GTAAC-5', 293, 3'-GAAAT-5', 356, 3'-GAAAT-5', 653, 3'-ATTAT-5', 719, 3'-ATTAT-5', 726, 3'-ATAAT-5', 729,
  11. inverse complement, positive strand, negative direction is SuccessablesPboxci+-.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 107, 3'-GATAC-5', 58, 3'-AAAAC-5', 67, 3'-GATAT-5', 75, 3'-GATAT-5', 109, 3'-GAAAC-5', 127, 3'-AAAAC-5', 165, 3'-GAAAC-5', 227, 3'-GTAAT-5', 248, 3'-AAAAC-5', 258, 3'-ATAAT-5', 270, 3'-AATAT-5', 272, 3'-GAAAC-5', 304, 3'-GAAAC-5', 313, 3'-AAAAC-5', 359, 3'-GTAAT-5', 397, 3'-GAAAC-5', 474, 3'-AAAAT-5', 488, 3'-AATAC-5', 490, 3'-AAAAT-5', 496, 3'-GTAAT-5', 534, 3'-AATAT-5', 603, 3'-GTAAC-5', 613, 3'-AAAAT-5', 631, 3'-AATAC-5', 633, 3'-AAAAT-5', 640, 3'-GTAAT-5', 670, 3'-AAAAT-5', 765, 3'-AATAC-5', 767, 3'-AAAAT-5', 774, 3'-GTAAT-5', 804, 3'-GTAAT-5', 1134, 3'-GAAAC-5', 1213, 3'-AAAAT-5', 1231, 3'-GTAAT-5', 1261, 3'-ATTAC-5', 1296, 3'-AAAAC-5', 1372, 3'-AAAAC-5', 1386, 3'-AAAAT-5', 1562, 3'-AATAC-5', 1564, 3'-GAAAC-5', 1583, 3'-GATAT-5', 1596, 3'-GAAAT-5', 1631, 3'-GAAAC-5', 1643, 3'-GAAAT-5', 1661, 3'-GATAC-5', 1666, 3'-GTAAT-5', 1707, 3'-ATTAT-5', 1724, 3'-AAAAT-5', 1738, 3'-AATAT-5', 1740, 3'-GTAAT-5', 1779, 3'-GAAAC-5', 1856, 3'-AAAAT-5', 1874, 3'-AATAC-5', 1876, 3'-AAAAT-5', 1884, 3'-GTAAT-5', 1914, 3'-AAAAT-5', 2061, 3'-GTAAT-5', 2088, 3'-GAAAT-5', 2158, 3'-AATAC-5', 2160, 3'-GATAC-5', 2178, 3'-AAAAT-5', 2185, 3'-GAAAC-5', 2283, 3'-AAAAT-5', 2301, 3'-AATAC-5', 2303, 3'-AAAAC-5', 2310, 3'-AAAAC-5', 2491, 3'-AAAAC-5', 2507, 3'-GAAAC-5', 2620, 3'-AATAT-5', 2638, 3'-AAAAT-5', 2646, 3'-GTAAT-5', 2675, 3'-GAAAT-5', 2747, 3'-AAAAC-5', 2840, 3'-AATAT-5', 2850, 3'-AAAAT-5', 2867, 3'-AATAT-5', 2869, 3'-AAAAT-5', 2930, 3'-GAAAC-5', 2958, 3'-AAAAC-5', 2969, 3'-GATAT-5', 2982, 3'-AAAAT-5', 3011, 3'-AAAAC-5', 3027, 3'-GTAAT-5', 3064, 3'-GAAAC-5', 3147, 3'-AAAAC-5', 3165, 3'-AAAAT-5', 3173, 3'-AAAAT-5', 3314, 3'-AAAAC-5', 3328, 3'-AAAAT-5', 3355, 3'-GATAT-5', 3466, 3'-ATTAC-5', 3469, 3'-AAAAC-5', 3510, 3'-ATAAT-5', 3537, 3'-AATAC-5', 3539, 3'-GATAC-5', 3545, 3'-GAAAC-5', 3592, 3'-ATAAT-5', 3657, 3'-AAAAT-5', 3768, 3'-GTAAT-5', 3973, 3'-AAAAT-5', 4069, 3'-ATAAT-5', 4076, 3'-AAAAT-5', 4088, 3'-AAAAT-5', 4219, 3'-ATAAT-5', 4222, 3'-ATAAT-5', 4225, 3'-AAAAC-5', 4311, 3'-AAAAC-5', 4396,
  12. inverse complement, positive strand, positive direction is SuccessablesPboxci++.bas, looking for 3'-(A/G)(A/T)(A/T)A(C/T)-5', 9, 3'-GATAT-5', 260, 3'-GAAAC-5', 507, 3'-AAAAT-5', 671, 3'-AAAAT-5', 682, 3'-ATAAT-5', 704, 3'-ATAAC-5', 721, 3'-AATAT-5', 727, 3'-GAAAC-5', 769, 3'-GTAAC-5', 871,
  13. inverse, negative strand, negative direction, is SuccessablesPboxi--.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 107, 3'-CTATG-5', 58, 3'-TTTTG-5', 67, 3'-CTATA-5', 75, 3'-CTATA-5', 109, 3'-CTTTG-5', 127, 3'-TTTTG-5', 165, 3'-CTTTG-5', 227, 3'-CATTA-5', 248, 3'-TTTTG-5', 258, 3'-TATTA-5', 270, 3'-TTATA-5', 272, 3'-CTTTG-5', 304, 3'-CTTTG-5', 313, 3'-TTTTG-5', 359, 3'-CATTA-5', 397, 3'-CTTTG-5', 474, 3'-TTTTA-5', 488, 3'-TTATG-5', 490, 3'-TTTTA-5', 496, 3'-CATTA-5', 534, 3'-TTATA-5', 603, 3'-CATTG-5', 613, 3'-TTTTA-5', 631, 3'-TTATG-5', 633, 3'-TTTTA-5', 640, 3'-CATTA-5', 670, 3'-TTTTA-5', 765, 3'-TTATG-5', 767, 3'-TTTTA-5', 774, 3'-CATTA-5', 804, 3'-CATTA-5', 1134, 3'-CTTTG-5', 1213, 3'-TTTTA-5', 1231, 3'-CATTA-5', 1261, 3'-TAATG-5', 1296, 3'-TTTTG-5', 1372, 3'-TTTTG-5', 1386, 3'-TTTTA-5', 1562, 3'-TTATG-5', 1564, 3'-CTTTG-5', 1583, 3'-CTATA-5', 1596, 3'-CTTTA-5', 1631, 3'-CTTTG-5', 1643, 3'-CTTTA-5', 1661, 3'-CTATG-5', 1666, 3'-CATTA-5', 1707, 3'-TAATA-5', 1724, 3'-TTTTA-5', 1738, 3'-TTATA-5', 1740, 3'-CATTA-5', 1779, 3'-CTTTG-5', 1856, 3'-TTTTA-5', 1874, 3'-TTATG-5', 1876, 3'-TTTTA-5', 1884, 3'-CATTA-5', 1914, 3'-TTTTA-5', 2061, 3'-CATTA-5', 2088, 3'-CTTTA-5', 2158, 3'-TTATG-5', 2160, 3'-CTATG-5', 2178, 3'-TTTTA-5', 2185, 3'-CTTTG-5', 2283, 3'-TTTTA-5', 2301, 3'-TTATG-5', 2303, 3'-TTTTG-5', 2310, 3'-TTTTG-5', 2491, 3'-TTTTG-5', 2507, 3'-CTTTG-5', 2620, 3'-TTATA-5', 2638, 3'-TTTTA-5', 2646, 3'-CATTA-5', 2675, 3'-CTTTA-5', 2747, 3'-TTTTG-5', 2840, 3'-TTATA-5', 2850, 3'-TTTTA-5', 2867, 3'-TTATA-5', 2869, 3'-TTTTA-5', 2930, 3'-CTTTG-5', 2958, 3'-TTTTG-5', 2969, 3'-CTATA-5', 2982, 3'-TTTTA-5', 3011, 3'-TTTTG-5', 3027, 3'-CATTA-5', 3064, 3'-CTTTG-5', 3147, 3'-TTTTG-5', 3165, 3'-TTTTA-5', 3173, 3'-TTTTA-5', 3314, 3'-TTTTG-5', 3328, 3'-TTTTA-5', 3355, 3'-CTATA-5', 3466, 3'-TAATG-5', 3469, 3'-TTTTG-5', 3510, 3'-TATTA-5', 3537, 3'-TTATG-5', 3539, 3'-CTATG-5', 3545, 3'-CTTTG-5', 3592, 3'-TATTA-5', 3657, 3'-TTTTA-5', 3768, 3'-CATTA-5', 3973, 3'-TTTTA-5', 4069, 3'-TATTA-5', 4076, 3'-TTTTA-5', 4088, 3'-TTTTA-5', 4219, 3'-TATTA-5', 4222, 3'-TATTA-5', 4225, 3'-TTTTG-5', 4311, 3'-TTTTG-5', 4396,
  14. inverse, negative strand, positive direction, is SuccessablesPboxi-+.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 9, 3'-CTATA-5', 260, 3'-CTTTG-5', 507, 3'-TTTTA-5', 671, 3'-TTTTA-5', 682, 3'-TATTA-5', 704, 3'-TATTG-5', 721, 3'-TTATA-5', 727, 3'-CTTTG-5', 769, 3'-CATTG-5', 871,
  15. inverse, positive strand, negative direction, is SuccessablesPboxi+-.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 54, 3'-TTTTG-5', 28, 3'-CTTTA-5', 48, 3'-CATTA-5', 153, 3'-CATTA-5', 173, 3'-TTTTA-5', 191, 3'-CTATG-5', 211, 3'-TTTTA-5', 217, 3'-TTATA-5', 219, 3'-TATTA-5', 236, 3'-TAATA-5', 249, 3'-TAATA-5', 271, 3'-CTTTA-5', 348, 3'-TTATG-5', 350, 3'-CTTTG-5', 409, 3'-CTTTG-5', 546, 3'-TAATA-5', 602, 3'-CTTTG-5', 682, 3'-CATTG-5', 886, 3'-CTTTG-5', 1146, 3'-CATTG-5', 1343, 3'-CAATA-5', 1362, 3'-TTTTG-5', 1433, 3'-CTATA-5', 1526, 3'-CTTTG-5', 1688, 3'-TAATA-5', 1708, 3'-TTTTA-5', 1728, 3'-CTTTA-5', 1734, 3'-CTTTG-5', 1791, 3'-CTTTG-5', 2100, 3'-CTTTG-5', 2217, 3'-CAATA-5', 2497, 3'-CTTTG-5', 2553, 3'-CAATA-5', 2849, 3'-TTTTA-5', 2854, 3'-CTATA-5', 2899, 3'-CATTA-5', 2951, 3'-TATTA-5', 2977, 3'-TATTA-5', 2998, 3'-TTTTA-5', 3021, 3'-CTTTG-5', 3076, 3'-CATTG-5', 3285, 3'-TTTTA-5', 3350, 3'-CATTA-5', 3436, 3'-TATTA-5', 3454, 3'-TATTA-5', 3468, 3'-TATTG-5', 3528, 3'-TAATA-5', 3538, 3'-TAATG-5', 3658, 3'-CTTTG-5', 3985, 3'-TAATA-5', 4077, 3'-TAATA-5', 4223, 3'-CTTTG-5', 4462, 3'-TTTTA-5', 4512, 3'-TATTA-5', 4538,
  16. inverse, positive strand, positive direction, is SuccessablesPboxi++.bas, looking for 3'-(C/T)(A/T)(A/T)T(A/G)-5', 6, 3'-CATTG-5', 293, 3'-CTTTA-5', 356, 3'-CTTTA-5', 653, 3'-TAATA-5', 719, 3'-TAATA-5', 726, 3'-TATTA-5', 729.

Pribnow boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/Pribnow and Pribnow boxes

"Although the first five bases of the conserved sequence are identical to the first five bases of the Pribnow box (TATAA), the sixth base of the Pribnow box is a 100 per cent conserved T (refs 15-17) while the 100 per cent conserved A found here is actually more similar to eukaryotic promoter sequences20."[20]

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated(1-5). These domains are the -35 sequence [M35 box] (5'-T-T-G-A-C-A) and the Pribnow box (5'-T-A-T-A-A-T) in the -10 region. Both domains are in close contact with the RNA polymerase during initiation of RNA synthesis (2,6)."[18]

For the Basic programs (starting with SuccessablesPrib.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPrib--.bas, looking for 3'-TATAAT-5', 2, 3'-TATAAT-5', 3454, 3'-TATAAT-5', 3468,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPrib-+.bas, looking for 3'-TATAAT-5', 1, 3'-TATAAT-5', 729,
  3. positive strand in the negative direction is SuccessablesPrib+-.bas, looking for 3'-TATAAT-5', 0,
  4. positive strand in the positive direction is SuccessablesPrib++.bas, looking for 3'-TATAAT-5', 0,
  5. complement, negative strand, negative direction is SuccessablesPribc--.bas, looking for 3'-ATATTA-5', 0,
  6. complement, negative strand, positive direction is SuccessablesPribc-+.bas, looking for 3'-ATATTA-5', 0,
  7. complement, positive strand, negative direction is SuccessablesPribc+-.bas, looking for 3'-ATATTA-5', 2, 3'-ATATTA-5', 3454, 3'-ATATTA-5', 3468,
  8. complement, positive strand, positive direction is SuccessablesPribc++.bas, looking for 3'-ATATTA-5', 1, 3'-ATATTA-5', 729,
  9. inverse complement, negative strand, negative direction is SuccessablesPribci--.bas, looking for 3'-ATTATA-5', 2, 3'-ATTATA-5', 272, 3'-ATTATA-5', 603,
  10. inverse complement, negative strand, positive direction is SuccessablesPribci-+.bas, looking for 3'-ATTATA-5', 1, 3'-ATTATA-5', 727,
  11. inverse complement, positive strand, negative direction is SuccessablesPribci+-.bas, looking for 3'-ATTATA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesPribci++.bas, looking for 3'-ATTATA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesPribi--.bas, looking for 3'-TAATAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesPribi-+.bas, looking for 3'-TAATAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesPribi+-.bas, looking for 3'-TAATAT-5', 2, 3'-TAATAT-5', 272, 3'-TAATAT-5', 603,
  16. inverse, positive strand, positive direction, is SuccessablesPribi++.bas, looking for 3'-TAATAT-5', 1, 3'-TAATAT-5', 727.

Prolamin boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/Prolamins and Prolamin boxes

"The BPBF [barley prolamin-box (P-box) binding factor] expressed in bacteria as a GST-fusion binds a P-box 5′-TGTAAAG-3′ [3'-TG(A/T)AAAG-5'] containing oligonucleotide derived from the promoter region of anHor2gene."[15]

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995). The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."[15]

For the Basic programs (starting with SuccessablesProl.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesProl1--.bas, looking for 3'-TG(A/T)AAAG-5', 1, 3'-TGTAAAG-5', 2884,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesProl1-+.bas, looking for 3'-TG(A/T)AAAG-5', 1, 3'-TGAAAAG-5', 489,
  3. positive strand in the negative direction is SuccessablesProl1+-.bas, looking for 3'-TG(A/T)AAAG-5', 1, 3'-TGAAAAG-5', 1627,
  4. positive strand in the positive direction is SuccessablesProl1++.bas, looking for 3'-TG(A/T)AAAG-5', 0,
  5. complement, negative strand, negative direction is SuccessablesProl1c--.bas, looking for 3'-AC(A/T)TTTC-5', 1, 3'-ACTTTTC-5', 1627,
  6. complement, negative strand, positive direction is SuccessablesProl1c-+.bas, looking for 3'-AC(A/T)TTTC-5', 0,
  7. complement, positive strand, negative direction is SuccessablesProl1c+-.bas, looking for 3'-AC(A/T)TTTC-5', 1, 3'-ACATTTC-5', 2884,
  8. complement, positive strand, positive direction is SuccessablesProl1c++.bas, looking for 3'-AC(A/T)TTTC-5', 1, 3'-ACTTTTC-5', 489,
  9. inverse complement, negative strand, negative direction is SuccessablesProl1ci--.bas, looking for 3'-CTTT(A/T)CA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesProl1ci-+.bas, looking for 3'-CTTT(A/T)CA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesProl1ci+-.bas, looking for 3'-CTTT(A/T)CA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesProl1ci++.bas, looking for 3'-CTTT(A/T)CA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesProl1i--.bas, looking for 3'-GAAA(A/T)GT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesProl1i-+.bas, looking for 3'-GAAA(A/T)GT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesProl1i+-.bas, looking for 3'-GAAA(A/T)GT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesProl1i++.bas, looking for 3'-GAAA(A/T)GT-5', 0.

Pyrimidine boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/Pyrimidines and Pyrimidine boxes

"Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5′-CCTTTT-3′."[11]

For the Basic programs (starting with SuccessablesPyr.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPyr--.bas, looking for 3'-CCTTTT-5', 3, 3'-CCTTTT-5', 2459, 3'-CCTTTT-5', 2927, 3'-CCTTTT-5', 2968,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPyr-+.bas, looking for 3'-CCTTTT-5', 1, 3'-CCTTTT-5', 135,
  3. positive strand in the negative direction is SuccessablesPyr+-.bas, looking for 3'-CCTTTT-5', 0,
  4. positive strand in the positive direction is SuccessablesPyr++.bas, looking for 3'-CCTTTT-5', 1, 3'-CCTTTT-5', 291,
  5. complement, negative strand, negative direction is SuccessablesPyrc--.bas, looking for 3'-GGAAAA-5', 0,
  6. complement, negative strand, positive direction is SuccessablesPyrc-+.bas, looking for 3'-GGAAAA-5', 1, 3'-GGAAAA-5', 291,
  7. complement, positive strand, negative direction is SuccessablesPyrc+-.bas, looking for 3'-GGAAAA-5', 3, 3'-GGAAAA-5', 2459, 3'-GGAAAA-5', 2927, 3'-GGAAAA-5', 2968,
  8. complement, positive strand, positive direction is SuccessablesPyrc++.bas, looking for 3'-GGAAAA-5', 1, 3'-GGAAAA-5', 135,
  9. inverse complement, negative strand, negative direction is SuccessablesPyrci--.bas, looking for 3'-AAAAGG-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesPyrci-+.bas, looking for 3'-AAAAGG-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesPyrci+-.bas, looking for 3'-AAAAGG-5', 4, 3'-AAAAGG-5', 105, 3'-AAAAGG-5', 1107, 3'-AAAAGG-5', 3345, 3'-AAAAGG-5', 3441,
  12. inverse complement, positive strand, positive direction is SuccessablesPyrci++.bas, looking for 3'-AAAAGG-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesPyri--.bas, looking for 3'-TTTTCC-5', 4, 3'-TTTTCC-5', 105, 3'-TTTTCC-5', 1107, 3'-TTTTCC-5', 3345, 3'-TTTTCC-5', 3441,
  14. inverse, negative strand, positive direction, is SuccessablesPyri-+.bas, looking for 3'-TTTTCC-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesPyri+-.bas, looking for 3'-TTTTCC-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesPyri++.bas, looking for 3'-TTTTCC-5', 0.

TACTAAC boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/TACTAAC and TACTAAC boxes

"The comparison of the two rp51 genes [...] suggests that this homology might be more extensive if one allows up to 3 bases to differ from a larger consensus sequence, ATTTACTAAC."[21]

"A consensus sequence TACTAA(C/T) was derived for the branch site of Dictyostelium introns."[22]

For the Basic programs (starting with SuccessablesTACT.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTACT--.bas, looking for 3'-TACTAA(C/T)-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTACT-+.bas, looking for 3'-TACTAA(C/T)-5', 0,
  3. positive strand in the negative direction is SuccessablesTACT+-.bas, looking for 3'-TACTAA(C/T)-5', 0,
  4. positive strand in the positive direction is SuccessablesTACT++.bas, looking for 3'-TACTAA(C/T)-5', 1, 3'-TACTAAT-5', 718,
  5. complement, negative strand, negative direction is SuccessablesTACTc--.bas, looking for 3'-ATGATT(A/G)-5', 0,
  6. complement, negative strand, positive direction is SuccessablesTACTc-+.bas, looking for 3'-ATGATT(A/G)-5', 1, 3'-ATGATTA-5', 718,
  7. complement, positive strand, negative direction is SuccessablesTACTc+-.bas, looking for 3'-ATGATT(A/G)-5', 0,
  8. complement, positive strand, positive direction is SuccessablesTACTc++.bas, looking for 3'-ATGATT(A/G)-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesTACTci--.bas, looking for 3'-(A/G)TTAGTA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesTACTci-+.bas, looking for 3'-(A/G)TTAGTA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesTACTci+-.bas, looking for 3'-(A/G)TTAGTA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesTACTci++.bas, looking for 3'-(A/G)TTAGTA-5', 1, 3'-ATTAGTA-5', 709,
  13. inverse, negative strand, negative direction, is SuccessablesTACTi--.bas, looking for 3'-(C/T)AATCAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesTACTi-+.bas, looking for 3'-(C/T)AATCAT-5', 1, 3'-TAATCAT-5', 709,
  15. inverse, positive strand, negative direction, is SuccessablesTACTi+-.bas, looking for 3'-(C/T)AATCAT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesTACTi++.bas, looking for 3'-(C/T)AATCAT-5', 0.

TATCCAC boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/TATCCACs and TATCCAC boxes

"Although this GARC [GA responsive complex] may not always be tripartite, most often it includes three sequence motifs, the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994)."[11]

For the Basic programs (starting with SuccessablesTATC.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTATC--.bas, looking for 3'-TATCCAC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTATC-+.bas, looking for 3'-TATCCAC-5', 0,
  3. positive strand in the negative direction is SuccessablesTATC+-.bas, looking for 3'-TATCCAC-5', 0,
  4. positive strand in the positive direction is SuccessablesTATC++.bas, looking for 3'-TATCCAC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesTATCc--.bas, looking for 3'-ATAGGTG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesTATCc-+.bas, looking for 3'-ATAGGTG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesTATCc+-.bas, looking for 3'-ATAGGTG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesTATCc++.bas, looking for 3'-ATAGGTG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesTATCci--.bas, looking for 3'-GTGGATA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesTATCci-+.bas, looking for 3'-GTGGATA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesTATCci+-.bas, looking for 3'-GTGGATA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesTATCci++.bas, looking for 3'-GTGGATA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesTATCi--.bas, looking for 3'-CACCTAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesTATCi-+.bas, looking for 3'-CACCTAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesTATCi+-.bas, looking for 3'-CACCTAT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesTATCi++.bas, looking for 3'-CACCTAT-5', 0.

X boxes

[edit | edit source]
Main resources: Gene transcriptions/Boxes/Xs and X boxes

"The so-called X (or X1) box in the promoter of the human MHC class II DRA gene is the binding site for a ubiquitous mammalian sequence-specific DNA-binding protein called RFX, NF-X, NF-Xc, or RFX1 (4,19,23,24,27)."[23]

"RFX is MDBP [...] the MDBP (RFX) recognition site region in the DRA promoter can be considered to extend from positions -100 to -112 [...] a possible binding site for MDBP which begins 88 bp after the first residue of the presumably full-length RFX1 (MDBP) cDNA (26). This site (RFX+88) is as follows: 5'-GTTGGCATGGCAAC-3'."[23]

For the Basic programs (starting with SuccessablesXbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesXbox--.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesXbox-+.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  3. positive strand in the negative direction is SuccessablesXbox+-.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  4. positive strand in the positive direction is SuccessablesXbox++.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesXboxc--.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesXboxc-+.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesXboxc+-.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesXboxc++.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesXboxci--.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesXboxci-+.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesXboxci+-.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesXboxci++.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesXboxi--.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesXboxi-+.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesXboxi+-.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesXboxi++.bas, looking for 3'-CAACGGTACGGTTG-5', 0.

Y boxes

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Main resources: Gene transcriptions/Boxes/Ys and Y boxes

The "Y-box [is] an inverted CCAAT box, in the promoter region of many genes; this domain is highly conserved in evolution [1, 3, 4]."[24]

On the template strand, the CAAT box consensus sequence is 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5'. An inverted CAAT box has the consensus sequence 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5'

For the Basic programs (starting with SuccessablesYbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesYbox--.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesYbox-+.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  3. positive strand in the negative direction is SuccessablesYbox+-.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  4. positive strand in the positive direction is SuccessablesYbox++.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  5. complement, negative strand, negative direction is SuccessablesYboxc--.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  6. complement, negative strand, positive direction is SuccessablesYboxc-+.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  7. complement, positive strand, negative direction is SuccessablesYboxc+-.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  8. complement, positive strand, positive direction is SuccessablesYboxc++.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesYboxci--.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesYboxci-+.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesYboxci+-.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesYboxci++.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesYboxi--.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesYboxi-+.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesYboxi+-.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesYboxi++.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0.

TATA boxes

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Main resources: Gene transcriptions/Boxes/TATAs and TATA boxes

The TATA box (also called Goldberg-Hogness box)[25] is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes;[2] approximately 24% of human genes contain a TATA box within the core promoter.[5]

The TATA box is a binding site of either general transcription factors or histones.

For the Basic programs (starting with SuccessablesTATA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTATA--.bas, looking for 3'-TATA-A/T-A-A/T-A/G-5', 2, 3'-TATATATA-5' at 1600 (or -2860 nts upstream from the TSS) and 3'-TATATAAA-5' at 1602 (or -2858 nts),
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTATA-+.bas, looking for 3'-TATA-A/T-A-A/T-A/G-5-5', 0,
  3. positive strand in the negative direction is SuccessablesTATA+-.bas, looking for 3'-TATA-A/T-A-A/T-A/G-5', 3, 3'-TATAAAAG-5' at 184 (or -4276 nts), 3'-TATAAAAG-5' at 223 (or -4237 nts), and 3'-TATATAAA-5' at 2874 (or -1586 nts),
  4. positive strand in the positive direction is SuccessablesTATA++.bas, looking for 3'-TATA-A/T-A-A/T-A/G-5-5', 0,
  5. complement, negative strand, negative direction is SuccessablesTATAc--.bas, looking for 3'-ATAT-A/T-T-A/T-C/T-5', 3, 3'-ATATTTTC-5', 184, 3'-ATATTTTC-5', 223, 3'-ATATATTT-5', 2874,
  6. complement, negative strand, positive direction is SuccessablesTATAc-+.bas, looking for 3'-ATAT-A/T-T-A/T-C/T-5', 0,
  7. complement, positive strand, negative direction is SuccessablesTATAc+-.bas, looking for 3'-ATAT-A/T-T-A/T-C/T-5', 2, 3'-ATATATAT-5', 1600, 3'-ATATATTT-5', 1602,
  8. complement, positive strand, positive direction is SuccessablesTATAc++.bas, looking for 3'-ATAT-A/T-T-A/T-C/T-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesTATAci--.bas, looking for 3'-C/T-A/T-T-A/T-TATA-5', 2, 3'-TATATATA-5', 1600, 3'-TTTATATA-5', 2871,
  10. inverse complement, negative strand, positive direction is Successables4EBEci-+.bas, looking for 3'-C/T-A/T-T-A/T-TATA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesTATAci+-.bas, looking for 3'-C/T-A/T-T-A/T-TATA-5', 1, 3'-TTTTTATA-5', 219,
  12. inverse complement, positive strand, positive direction is SuccessablesTATAci++.bas, looking for 3'-C/T-A/T-T-A/T-TATA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesTATAi--.bas, looking for 3'-A/G-A/T-A-A/T-A-T-A-T-5', 1, 3'-AAAAATAT-5', 219,
  14. inverse, negative strand, positive direction, is SuccessablesTATAi-+.bas, looking for 3'-A/G-A/T-A-A/T-A-T-A-T-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesTATAi+-.bas, looking for 3'-A/G-A/T-A-A/T-A-T-A-T-5', 2, 3'-ATATATAT-5', 1600, 3'-AAATATAT-5', 2871,
  16. inverse, positive strand, positive direction, is SuccessablesTATAi++.bas, looking for 3'-A/G-A/T-A-A/T-A-T-A-T-5', 0.

Complements of and inverted TATA boxes may not have been reported as yet.

For number one, these are way outside the core promoter and may apply to an isoform between these two genes.

For number three, all of these are way outside the core promoter in the distal promoter at best and most likely relate to one or more isoforms on the positive strand between ZSCAN22 to A1BG.

Downstream TFIIB recognition

[edit | edit source]
Main resources: Gene transcriptions/Downstream TFIIB recognition elements and Downstream TFIIB recognition

The downstream TFIIB recognition element (dBRE) has a consensus sequence in the transcription direction on the template strand of 3'-RTDKKKK-5', using degenerate nucleotides, or 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5'.[26]

dBRE is cis-TATA box, between the TATA box and the Inr or transcription start site (TSS) and trans-TSS.[26]

For the Basic programs (starting with SuccessablesdBRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesdBRE--.bas, looking for 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5', 59, 3'-ATTTTGT-5', 68, 3'-ATATGTT-5', 113, 3'-GTTTTGT-5', 166, 3'-ATATTTT-5', 183, 3'-ATATTTT-5', 222, 3'-GTTTTGG-5', 259, 3'-ATGTTTT-5', 485, 3'-GTTTTTT-5', 487, 3'-ATTGGGG-5', 616, 3'-ATGTTTT-5', 637, 3'-GTTTTTT-5', 639, 3'-ATGTTTT-5', 771, 3'-GTTTTTT-5', 773, 3'-GTGTGGT-5', 883, 3'-GTTTTTT-5', 928, 3'-GTTTTTT-5', 1094, 3'-ATGTTTT-5', 1228, 3'-GTTTTTT-5', 1230, 3'-GTTTTTG-5', 1386, 3'-GTTTGTT-5', 1392, 3'-GTTTTTT-5', 1396, 3'-GTTGGGT-5', 1409, 3'-GTTGGGT-5', 1516, 3'-GTTTGTG-5', 1540, 3'-ATGTTTT-5', 1880, 3'-GTTTTTT-5', 1882, 3'-GTTTTTT-5', 2038, 3'-ATGTTTT-5', 2182, 3'-GTTTTTT-5', 2184, 3'-ATGTTTT-5', 2307, 3'-GTTTTTT-5', 2309, 3'-GTGTGGT-5', 2419, 3'-GTTTGTT-5', 2484, 3'-GTTTGTT-5', 2488, 3'-ATATGTT-5', 2642, 3'-ATGTTTT-5', 2644, 3'-GTGGGGT-5', 2764, 3'-GTTGGGT-5', 2846, 3'-ATATTTG-5', 2875, 3'-GTAGTTT-5', 2890, 3'-ATTTTTT-5', 3026, 3'-GTGGGTT-5', 3136, 3'-ATTTTTG-5', 3165, 3'-GTATTTT-5', 3171, 3'-GTTTTTG-5', 3328, 3'-ATTTGTT-5', 3338, 3'-ATTTGGT-5', 3365, 3'-ATTTGGT-5', 3484, 3'-GTAGTTG-5', 3523, 3'-ATGGTGG-5', 3740, 3'-GTGTTTT-5', 3767, 3'-ATGTTTT-5', 4066, 3'-GTTTTTT-5', 4068, 3'-GTTGTGT-5', 4196, 3'-ATGTTTT-5', 4216, 3'-GTTTTTT-5', 4218, 3'-GTTTTTT-5', 4378, 3'-GTGGGGT-5', 4446, 3'-GTAGGTG-5', 4458,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesdBRE-+.bas, looking for 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5', 8, 3'-GTGTGGG-5', 11, 3'-GTGGTGG-5', 377, 3'-GTGTGGT-5', 528, 3'-GTGGTGT-5', 530, 3'-GTGGTTT-5', 669, 3'-ATTGTTG-5', 734, 3'-ATGGGGG-5', 786, 3'-GTGGGGT-5', 958,
  3. positive strand in the negative direction is SuccessablesdBRE+-.bas, looking for 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5', 31, 3'-ATATGTT-5', 43, 3'-ATATGGG-5', 78, 3'-ATGGGGT-5', 204, 3'-ATGTTTT-5', 215, 3'-ATATGGT-5', 606, 3'-ATGGTGT-5', 608, 3'-ATGTGGT-5', 788, 3'-GTGGTGG-5', 790, 3'-GTGGTGT-5', 793, 3'-ATTGGGT-5', 1047, 3'-GTGGGTG-5', 1163, 3'-GTGGTGG-5', 1247, 3'-GTGGTGT-5', 1477, 3'-GTGGTGG-5', 1900, 3'-GTGGTGG-5', 1903, 3'-GTGGGTG-5', 2332, 3'-GTGTGGT-5', 2659, 3'-GTGGTGG-5', 2661, 3'-ATATTTT-5', 2853, 3'-GTGGTGG-5', 3050, 3'-GTGTGGT-5', 3187, 3'-GTGGTGG-5', 3189, 3'-GTGGTGG-5', 3192, 3'-GTGGGTG-5', 3195, 3'-ATTGGTT-5', 3531, 3'-GTGGTTG-5', 3605, 3'-ATGGGGT-5', 3802, 3'-ATGTGGT-5', 3811, 3'-GTGTTGG-5', 3942, 3'-GTTGGTT-5', 3944, 3'-ATGGTGG-5', 4110,
  4. positive strand in the positive direction is SuccessablesdBRE++.bas, looking for 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5', 5, 3'-GTAGGGT-5', 192, 3'-GTGTGGT-5', 386, 3'-GTTTGTG-5', 818, 3'-GTGGGGT-5', 847, 3'-GTGGGGT-5', 889,
  5. complement, negative strand, negative direction is SuccessablesdBREc--.bas, looking for 3'-C/T-A-A/C/T-A/C-A/C-A/C-A/C-5', 31, 3'-TATACAA-5', 43, 3'-TATACCC-5', 78, 3'-TACCCCA-5', 204, 3'-TACAAAA-5', 215, 3'-TATACCA-5', 606, 3'-TACCACA-5', 608, 3'-TACACCA-5', 788, 3'-CACCACC-5', 790, 3'-CACCACA-5', 793, 3'-TAACCCA-5', 1047, 3'-CACCCAC-5', 1163, 3'-CACCACC-5', 1247, 3'-CACCACA-5', 1477, 3'-CACCACC-5', 1900, 3'-CACCACC-5', 1903, 3'-CACCCAC-5', 2332, 3'-CACACCA-5', 2659, 3'-CACCACC-5', 2661, 3'-TATAAAA-5', 2853, 3'-CACCACC-5', 3050, 3'-CACACCA-5', 3187, 3'-CACCACC-5', 3189, 3'-CACCACC-5', 3192, 3'-CACCCAC-5', 3195, 3'-TAACCAA-5', 3531, 3'-CACCAAC-5', 3605, 3'-TACCCCA-5', 3802, 3'-TACACCA-5', 3811, 3'-CACAACC-5', 3942, 3'-CAACCAA-5', 3944, 3'-TACCACC-5', 4110,
  6. complement, negative strand, positive direction is SuccessablesdBREc-+.bas, looking for 3'-C/T-A-A/C/T-A/C-A/C-A/C-A/C-5', 5, 3'-CATCCCA-5', 192, 3'-CACACCA-5', 386, 3'-CAAACAC-5', 818, 3'-CACCCCA-5', 847, 3'-CACCCCA-5', 889,
  7. complement, positive strand, negative direction is SuccessablesdBREc+-.bas, looking for 3'-C/T-A-A/C/T-A/C-A/C-A/C-A/C-5', 59, 3'-TAAAACA-5', 68, 3'-TATACAA-5', 113, 3'-CAAAACA-5', 166, 3'-TATAAAA-5', 183, 3'-TATAAAA-5', 222, 3'-CAAAACC-5', 259, 3'-TACAAAA-5', 485, 3'-CAAAAAA-5', 487, 3'-TAACCCC-5', 616, 3'-TACAAAA-5', 637, 3'-CAAAAAA-5', 639, 3'-TACAAAA-5', 771, 3'-CAAAAAA-5', 773, 3'-CACACCA-5', 883, 3'-CAAAAAA-5', 928, 3'-CAAAAAA-5', 1094, 3'-TACAAAA-5', 1228, 3'-CAAAAAA-5', 1230, 3'-CAAAAAC-5', 1386, 3'-CAAACAA-5', 1392, 3'-CAAAAAA-5', 1396, 3'-CAACCCA-5', 1409, 3'-CAACCCA-5', 1516, 3'-CAAACAC-5', 1540, 3'-TACAAAA-5', 1880, 3'-CAAAAAA-5', 1882, 3'-CAAAAAA-5', 2038, 3'-TACAAAA-5', 2182, 3'-CAAAAAA-5', 2184, 3'-TACAAAA-5', 2307, 3'-CAAAAAA-5', 2309, 3'-CACACCA-5', 2419, 3'-CAAACAA-5', 2484, 3'-CAAACAA-5', 2488, 3'-TATACAA-5', 2642, 3'-TACAAAA-5', 2644, 3'-CACCCCA-5', 2764, 3'-CAACCCA-5', 2846, 3'-TATAAAC-5', 2875, 3'-CATCAAA-5', 2890, 3'-TAAAAAA-5', 3026, 3'-CACCCAA-5', 3136, 3'-TAAAAAC-5', 3165, 3'-CATAAAA-5', 3171, 3'-CAAAAAC-5', 3328, 3'-TAAACAA-5', 3338, 3'-TAAACCA-5', 3365, 3'-TAAACCA-5', 3484, 3'-CATCAAC-5', 3523, 3'-TACCACC-5', 3740, 3'-CACAAAA-5', 3767, 3'-TACAAAA-5', 4066, 3'-CAAAAAA-5', 4068, 3'-CAACACA-5', 4196, 3'-TACAAAA-5', 4216, 3'-CAAAAAA-5', 4218, 3'-CAAAAAA-5', 4378, 3'-CACCCCA-5', 4446, 3'-CATCCAC-5', 4458,
  8. complement, positive strand, positive direction is SuccessablesdBREc++.bas, looking for 3'-C/T-A-A/C/T-A/C-A/C-A/C-A/C-5', 8, 3'-CACACCC-5', 11, 3'-CACCACC-5', 377, 3'-CACACCA-5', 528, 3'-CACCACA-5', 530, 3'-CACCAAA-5', 669, 3'-TAACAAC-5', 734, 3'-TACCCCC-5', 786, 3'-CACCCCA-5', 958,
  9. inverse complement, negative strand, negative direction is SuccessablesdBREci--.bas, looking for 3'-A/C-A/C-A/C-A/C-A/C/T-A-C/T-5', 7, 3'-ACCACAC-5', 609, 3'-ACACCAC-5', 789, 3'-CACACAT-5', 796, 3'-AACCCAC-5', 1048, 3'-CCAAAAT-5', 3350, 3'-AACCAAC-5', 3532, 3'-CACCAAC-5', 3605,
  10. inverse complement, negative strand, positive direction is SuccessablesdBREci-+.bas, looking for 3'-A/C-A/C-A/C-A/C-A/C/T-A-C/T-5', 1, 3'-ACCCCAT-5', 781,
  11. inverse complement, positive strand, negative direction is SuccessablesdBREci+-.bas, looking for 3'-A/C-A/C-A/C-A/C-A/C/T-A-C/T-5', 15, 3'-AAACAAT-5', 230, 3'-AAAACAT-5', 361, 3'-CCAACAT-5', 1205, 3'-CAAAAAC-5', 1386, 3'-CAAACAC-5', 1540, 3'-AAAATAT-5', 1740, 3'-ACAAAAC-5', 2491, 3'-CCAACAT-5', 2612, 3'-AAAAAAT-5', 2930, 3'-AAAAAAC-5', 3027, 3'-CAAAAAC-5', 3328, 3'-AAACCAC-5', 3366, 3'-CAACTAT-5', 3526, 3'-CCCATAC-5', 3857, 3'-AACCCAT-5', 4454,
  12. inverse complement, positive strand, positive direction is SuccessablesdBREci++.bas, looking for 3'-A/C-A/C-A/C-A/C-A/C/T-A-C/T-5', 2, 3'-ACACCAC-5', 205, 3'-AAACCAC-5', 510,
  13. inverse, negative strand, negative direction, is SuccessablesdBREi--.bas, looking for 3'-G/T-G/T-G/T-G/T-A/G/T-T-A/G-5', 15, 3'-TTTGTTA-5', 230, 3'-TTTTGTA-5', 361, 3'-GGTTGTA-5', 1205, 3'-GTTTTTG-5', 1386, 3'-GTTTGTG-5', 1540, 3'-TTTTATA-5', 1740, 3'-TGTTTTG-5', 2491, 3'-GGTTGTA-5', 2612, 3'-TTTTTTA-5', 2930, 3'-TTTTTTG-5', 3027, 3'-GTTTTTG-5', 3328, 3'-TTTGGTG-5', 3366, 3'-GTTGATA-5', 3526, 3'-GGGTATG-5', 3857, 3'-TTGGGTA-5', 4454,
  14. inverse, negative strand, positive direction, is SuccessablesdBREi-+.bas, looking for 3'-G/T-G/T-G/T-G/T-A/G/T-T-A/G-5', 2, 3'-TGTGGTG-5', 205, 3'-TTTGGTG-5', 510,
  15. inverse, positive strand, negative direction, is SuccessablesdBREi+-.bas, looking for 3'-G/T-G/T-G/T-G/T-A/G/T-T-A/G-5', 7, 3'-TGGTGTG-5', 609, 3'-TGTGGTG-5', 789, 3'-GTGTGTA-5', 796, 3'-TTGGGTG-5', 1048, 3'-GGTTTTA-5', 3350, 3'-TTGGTTG-5', 3532, 3'-GTGGTTG-5', 3605,
  16. inverse, positive strand, positive direction, is SuccessablesdBREi++.bas, looking for 3'-G/T-G/T-G/T-G/T-A/G/T-T-A/G-5', 1, 3'-TGGGGTA-5', 781.

X core promoter element 1

[edit | edit source]
Main resources: Gene transcriptions/X core promoter element 1 and X core promoter element 1

The core promoter element X core promoter element 1 (XCPE1) directs activator-, mediator-, protein-dependent but TFIID-independent RNA polymerase II transcription from TATA box-less promoters.[27]

For the Basic programs (starting with SuccessablesXCPE1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesXCPE1--.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 1, 3'-TGGTGGGACC-5', 3744,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesXCPE1-+.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 0,
  3. positive strand in the negative direction is SuccessablesXCPE1+-.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 0,
  4. positive strand in the positive direction is SuccessablesXCPE1++.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 0,
  5. complement, negative strand, negative direction is SuccessablesXCPE1c--.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 0,
  6. complement, negative strand, positive direction is SuccessablesXCPE1c-+.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 0,
  7. complement, positive strand, negative direction is SuccessablesXCPE1c+-.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 1, 3'-ACCACCCTGG-5', 3744,
  8. complement, positive strand, positive direction is SuccessablesXCPE1c++.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesXCPE1ci--.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesXCPE1ci-+.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesXCPE1ci+-.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 1, 3'-GCTCCCACCT-5', 392,
  12. inverse complement, positive strand, positive direction is SuccessablesXCPE1ci++.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesXCPE1i--.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 1, 3'-CGAGGGTGGA-5', 392,
  14. inverse, negative strand, positive direction, is SuccessablesXCPE1i-+.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 1, 3'-CCAGGGTGGG-5', 102,
  15. inverse, positive strand, negative direction, is SuccessablesXCPE1i+-.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesXCPE1i++.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 0.

Motif ten elements

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Main resources: Gene transcriptions/Elements/Motif ten and Motif ten elements

The motif ten element (MTE) is a downstream core promoter element that "promotes transcription by RNA polymerase II when it is located precisely at positions +18 to +27 relative to A+1 in the initiator (Inr) element."[28]

For the Basic programs (starting with SuccessablesMTE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extension of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesMTE--.bas, looking for 3'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesMTE-+.bas, looking for 3'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-5', 0,
  3. positive strand in the negative direction is SuccessablesMTE+-.bas, looking for 3'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-5', 0,
  4. positive strand in the positive direction is SuccessablesMTE++.bas, looking for 3'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-5', 0,
  5. complement, negative strand, negative direction is SuccessablesMTEc--.bas, looking for 3'-G-C/G-T-C/T-G-C/G-C/G-T-T-G-C-C/G-5', 0,
  6. complement, negative strand, positive direction is SuccessablesMTEc-+.bas, looking for 3'-G-C/G-T-C/T-G-C/G-C/G-T-T-G-C-C/G-5', 0,
  7. complement, positive strand, negative direction is SuccessablesMTEc+-.bas, looking for 3'-G-C/G-T-C/T-G-C/G-C/G-T-T-G-C-C/G-5', 0,
  8. complement, positive strand, positive direction is SuccessablesMTEc++.bas, looking for 3'-G-C/G-T-C/T-G-C/G-C/G-T-T-G-C-C/G-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesMTEci--.bas, looking for 3'-C/G-C-G-T-T-C/G-C/G-G-C/T-T-C/G-G-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesMTEci-+.bas, looking for 3'-C/G-C-G-T-T-C/G-C/G-G-C/T-T-C/G-G-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesMTEci+-.bas, looking for 3'-C/G-C-G-T-T-C/G-C/G-G-C/T-T-C/G-G-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesMTEci++.bas, looking for 3'-C/G-C-G-T-T-C/G-C/G-G-C/T-T-C/G-G-5', 0,
  13. inverse, negative strand, negative direction, is SuccessableMTEi--.bas, looking for 3'-C/G-G-C-A-A-C/G-C/G-C-A/G-A-C/G-C-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesMTEi-+.bas, looking for 3'-C/G-G-C-A-A-C/G-C/G-C-A/G-A-C/G-C-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesMTEi+-.bas, looking for 3'-C/G-G-C-A-A-C/G-C/G-C-A/G-A-C/G-C-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesMTEi++.bas, looking for 3'-C/G-G-C-A-A-C/G-C/G-C-A/G-A-C/G-C-5', 0.

GAAC elements

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Main resources: Gene transcriptions/Elements/GAAC and GAAC elements

The GAAC element is usually a core promoter element containing guanine (G), adenine (A), and cytosine (C), "able to direct a new transcription start site 2-7 bases downstream of itself, independent of TATA and Inr regions."[29]

For the Basic programs (starting with SuccessablesGAAC.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGAAC--.bas, looking for 3'-G-A-A-C-T-5', 13, 3'-GAACT-5', 843, 3'-GAACT-5', 1009, 3'-GAACT-5', 1300, 3'-GAACT-5', 2127, 3'-GAACT-5', 2379, 3'-GAACT-5', 2580, 3'-GAACT-5', 2714, 3'-GAACT-5', 3103, 3'-GAACT-5', 3242, 3'-GAACT-5', 3401, 3'-GAACT-5', 3571, 3'-GAACT-5', 4012, 3'-GAACT-5', 4294,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGAAC-+.bas, looking for 3'-G-A-A-C-T-5', 1, 3'-GAACT-5', 609,
  3. positive strand in the negative direction is SuccessablesGAAC+-.bas, looking for 3'-G-A-A-C-T-5', 2, 3'-GAACT-5', 1685, 3'-GAACT-5', 3460,
  4. positive strand in the positive direction is SuccessablesGAAC++.bas, looking for 3'-G-A-A-C-T-5', 2, 3'-GAACT-5', 577, 3'-GAACT-5', 692,
  5. complement, negative strand, negative direction is SuccessablesGAACc--.bas, looking for 3'-C-T-T-G-A-5', 2, 3'-CTTGA-5', 1685, 3'-CTTGA-5', 3460,
  6. complement, negative strand, positive direction is SuccessablesGAACc-+.bas, looking for 3'-C-T-T-G-A-5', 2, 3'-CTTGA-5', 577, 3'-CTTGA-5', 692,
  7. complement, positive strand, negative direction is SuccessablesGAACc+-.bas, looking for 3'-C-T-T-G-A-5', 13, 3'-CTTGA-5', 843, 3'-CTTGA-5', 1009, 3'-CTTGA-5', 1300, 3'-CTTGA-5', 2127, 3'-CTTGA-5', 2379, 3'-CTTGA-5', 2580, 3'-CTTGA-5', 2714, 3'-CTTGA-5', 3103, 3'-CTTGA-5', 3242, 3'-CTTGA-5', 3401, 3'-CTTGA-5', 3571, 3'-CTTGA-5', 4012, 3'-CTTGA-5', 4294,
  8. complement, positive strand, positive direction is SuccessablesGAACc++.bas, looking for 3'-C-T-T-G-A-5', 1, 3'-CTTGA-5', 609,
  9. inverse complement, negative strand, negative direction is SuccessablesGAACci--.bas, looking for 3'-A-G-T-T-C-5', 3, 3'-AGTTC-5', 3844, 3'-AGTTC-5', 4027, 3'-AGTTC-5', 4178,
  10. inverse complement, negative strand, positive direction is SuccessablesGAACci-+.bas, looking for 3'-A-G-T-T-C-5', 1, 3'-AGTTC-5', 761,
  11. inverse complement, positive strand, negative direction is SuccessablesGAACci+-.bas, looking for 3'-A-G-T-T-C-5', 6, 3'-AGTTC-5', 253, 3'-AGTTC-5', 719, 3'-AGTTC-5', 1177, 3'-AGTTC-5', 4024, 3'-AGTTC-5', 4175, 3'-AGTTC-5', 4417,
  12. inverse complement, positive strand, positive direction is SuccessablesGAACci++.bas, looking for 3'-A-G-T-T-C-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGAACi--.bas, looking for 3'-T-C-A-A-G-5', 6, 3'-TCAAG-5', 253, 3'-TCAAG-5', 719, 3'-TCAAG-5', 1177, 3'-TCAAG-5', 4024, 3'-TCAAG-5', 4175, 3'-TCAAG-5', 4417,
  14. inverse, negative strand, positive direction, is SuccessablesGAACi-+.bas, looking for 3'-T-C-A-A-G-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGAACi+-.bas, looking for 3'-T-C-A-A-G-5', 3, 3'-TCAAG-5', 3844, 3'-TCAAG-5', 4027, 3'-TCAAG-5', 4178,
  16. inverse, positive strand, positive direction, is SuccessablesGAACi++.bas, looking for 3'-T-C-A-A-G-5', 1, 3'-TCAAG-5', 761.

Initiator elements

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Main resources: Gene transcriptions/Initiator elements and Initiator elements

"RNA pol II itself recognizes features of the Inr which might assist the correct positioning of the polymerase on the promoter (Carcamo et al., 1991; Weis and Reinberg, 1997)."[3][30][31]

"[T]he initiator (INR) element located at, or immediately adjacent to, the TSS, ... is recognized by the TBP-associated factors TAF1 and TAF2 of the TFIID complex"[5] "[T]wo [non-Inr] motifs - M3 (SCGGAAGY) and M22 (TGCGCANK) - ... occur preferentially in human TATA-less core promoters."[5]

"[T]ranscription does not need to begin at the +1 nucleotide for the Inr to function. RNA polymerase II has been redirected to alternative start sites by reducing ATP concentrations within a nuclear extract, by altering the spacing between the TATA and Inr in a promoter containing both elements, and by dinucleotide initiation strategies"[2].

The wider consensus sequence of 3'-YYRNWYY-5' allows a G at the TSS but at most only allows two Gs in a row.[32]

The "sharp difference in the specificity of the Inr consensus between Drosophila and mammals suggests that mammalian transcription factors have evolved to function with a broader range of Inr sequences than Drosophila transcription factors. This property may be related to the prevalence of dispersed core promoters in mammals but not in Drosophila."[32]

For the Basic programs (starting with SuccessablesInr.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesInr--.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 121, 3'-TTGTTCC-5', 71, 3'-CTATACC-5', 77, 3'-CCGTTTC-5', 93, 3'-CCGTACT-5', 124, 3'-CCATATT-5', 181, 3'-CTACATT-5', 247, 3'-TTGGTCC-5', 262, 3'-TTATACT-5', 274, 3'-TCACTCT-5', 301, 3'-CTGCTTT-5', 312, 3'-CCGGTTC-5', 419, 3'-CCAGTCC-5', 441, 3'-TCGGACC-5', 459, 3'-TTGTATC-5', 468, 3'-TCACTTT-5', 473, 3'-TCGGACC-5', 508, 3'-CCGGTTC-5', 556, 3'-CCAGTCC-5', 578, 3'-TTATACC-5', 605, 3'-CCGGTCC-5', 648, 3'-CCGGTTC-5', 692, 3'-CCAGTCC-5', 714, 3'-TCGGACT-5', 732, 3'-TCGCACC-5', 741, 3'-CTACACC-5', 787, 3'-TCGGTTC-5', 874, 3'-TCGGACC-5', 899, 3'-TCGCTCT-5', 913, 3'-TCGGTCC-5', 948, 3'-CCGTACC-5', 953, 3'-TTAGTCC-5', 984, 3'-TTGGACC-5', 1015, 3'-TCACTCT-5', 1079, 3'-TCGGACC-5', 1198, 3'-TTGTACC-5', 1207, 3'-CCACTTT-5', 1212, 3'-CCGCACC-5', 1244, 3'-TTGGATC-5', 1306, 3'-TCAGACC-5', 1356, 3'-TTATTCT-5', 1365, 3'-TCGTTTT-5', 1371, 3'-TTGTTTT-5', 1394, 3'-CCACACT-5', 1479, 3'-TTGCTTC-5', 1555, 3'-CCGTTTT-5', 1561, 3'-TTACTTT-5', 1582, 3'-TTGGATT-5', 1591, 3'-TTAATTT-5', 1697, 3'-TTATACC-5', 1742, 3'-CCGCACC-5', 1897, 3'-CCGTACT-5', 1953, 3'-TTGGACC-5', 1959, 3'-TCGGACC-5', 2009, 3'-TCGTTCT-5', 2023, 3'-TTACACC-5', 2065, 3'-CCGGTCC-5', 2077, 3'-TCACATT-5', 2087, 3'-TCAAACT-5', 2141, 3'-TTGTACC-5', 2152, 3'-CCGCTTT-5', 2157, 3'-CCAGTCC-5', 2250, 3'-TCAAACT-5', 2257, 3'-TCGGACC-5', 2268, 3'-TCGTACC-5', 2277, 3'-CCACTTT-5', 2282, 3'-TTGGACC-5', 2385, 3'-TCGGACC-5', 2435, 3'-TCACTCT-5', 2449, 3'-TCGTTTT-5', 2476, 3'-TTGTTTT-5', 2490, 3'-TCATTCT-5', 2503, 3'-CCGGTCC-5', 2519, 3'-CCAGTCC-5', 2587, 3'-TCACACC-5', 2605, 3'-TTGTACC-5', 2614, 3'-CCACTTT-5', 2619, 3'-TCACACC-5', 2658, 3'-TTGGACC-5', 2720, 3'-TCGGACC-5', 2770, 3'-TCGTACT-5', 2784, 3'-TTGATTC-5', 2914, 3'-CCGATTT-5', 3009, 3'-TTGATTC-5', 3031, 3'-CCGCACC-5', 3047, 3'-TCGGACC-5', 3128, 3'-TTGTTCC-5', 3141, 3'-CCACTTT-5', 3146, 3'-TTGTATT-5', 3169, 3'-CCACACC-5', 3186, 3'-TCGGTTC-5', 3273, 3'-TCGGACC-5', 3298, 3'-TTGTTCT-5', 3307, 3'-TCGTTTT-5', 3313, 3'-TTGTTCT-5', 3340, 3'-TCGTTCT-5', 3374, 3'-CCGAACT-5', 3401, 3'-CCGTATC-5', 3446, 3'-TTGATCT-5', 3463, 3'-TTGGTCT-5', 3486, 3'-CTGTTCT-5', 3759, 3'-CTACACC-5', 3810, 3'-CTGGTCC-5', 3871, 3'-TCATTCT-5', 3893, 3'-CTACTTT-5', 3922, 3'-CCGGTCC-5', 3951, 3'-TCGGACC-5', 4037, 3'-TTGTATC-5', 4046, 3'-TCACTCT-5', 4051, 3'-TTACACT-5', 4092, 3'-CCGGTCC-5', 4102, 3'-CCGTACC-5', 4107, 3'-CCGGTCC-5', 4170, 3'-TCGAACC-5', 4188, 3'-TCACTCT-5', 4202, 3'-TCGGTCT-5', 4233, 3'-CTGCACC-5', 4238, 3'-TCGGACC-5', 4300, 3'-CCAGTTT-5', 4309, 3'-TCGGACC-5', 4349, 3'-TCACACT-5', 4361, 3'-TTACTCC-5', 4557,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesInr-+.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 9, 3'-TCACACT-5', 68, 3'-CCAGACC-5', 111, 3'-CTGTTCC-5', 186, 3'-TCACACC-5', 385, 3'-TCATTTT-5', 681, 3'-TCACTCT-5', 689, 3'-TTGATTT-5', 695, 3'-TTAGTTT-5', 700, 3'-CTGCACC-5', 904,
  3. positive strand in the negative direction is SuccessablesInr+-.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 40, 3'-CTGAATT-5', 20, 3'-TTGGACC-5', 32, 3'-CTGCATT-5', 152, 3'-TTGAACC-5', 846, 3'-TCACACC-5', 882, 3'-TTGAACC-5', 1012, 3'-TCACTCC-5', 1058, 3'-TCACACC-5', 1128, 3'-TTGAACC-5', 1303, 3'-TTGCACC-5', 1339, 3'-TTGCACT-5', 1347, 3'-CCAGTCT-5', 1354, 3'-CCATTTC-5', 1380, 3'-TCGCTCT-5', 1450, 3'-CTATATC-5', 1528, 3'-TTATTTT-5', 1727, 3'-CTGCACT-5', 2000, 3'-CTACTCC-5', 2352, 3'-TTGAACC-5', 2382, 3'-TCACACC-5', 2418, 3'-CTGCACT-5', 2426, 3'-TTGAATC-5', 2708, 3'-TTGAACC-5', 2717, 3'-CTGCACC-5', 2761, 3'-TTGAACC-5', 3245, 3'-TTGCACT-5', 3289, 3'-CCAGATC-5', 3488, 3'-CTGCTCC-5', 3582, 3'-CCATTTC-5', 3688, 3'-CTGGACT-5', 3747, 3'-CTGAACC-5', 3784, 3'-CCATACC-5', 3858, 3'-TCACACC-5', 3967, 3'-CCGGACT-5', 4327, 3'-CTGCACT-5', 4340, 3'-CCAGTTC-5', 4417, 3'-CCACTCC-5', 4425, 3'-CCACTTT-5', 4461, 3'-TCACATT-5', 4533, 3'-TTAATTC-5', 4542,
  4. positive strand in the positive direction is SuccessablesInr++.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 16, 3'-CTACTCC-5', 39, 3'-CCGATCC-5', 45, 3'-TCGATCC-5', 83, 3'-CTGGTCT-5', 109, 3'-TCACACT-5', 155, 3'-CCACTCC-5', 208, 3'-CCGGACC-5', 240, 3'-CCGGACC-5', 319, 3'-CTGGACC-5', 348, 3'-TCACTCC-5', 439, 3'-TCAGACT-5', 485, 3'-TCACACC-5', 527, 3'-CCACACT-5', 532, 3'-TTACTCC-5', 657, 3'-CTACTCC-5', 663, 3'-CTAAATC-5', 697,
  5. complement, negative strand, negative direction is SuccessablesInrc--.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 40, 3'-GACTTAA-5', 20, 3'-AACCTGG-5', 32, 3'-GACGTAA-5', 152, 3'-AACTTGG-5', 846, 3'-AGTGTGG-5', 882, 3'-AACTTGG-5', 1012, 3'-AGTGAGG-5', 1058, 3'-AGTGTGG-5', 1128, 3'-AACTTGG-5', 1303, 3'-AACGTGG-5', 1339, 3'-AACGTGA-5', 1347, 3'-GGTCAGA-5', 1354, 3'-GGTAAAG-5', 1380, 3'-AGCGAGA-5', 1450, 3'-GATATAG-5', 1528, 3'-AATAAAA-5', 1727, 3'-GACGTGA-5', 2000, 3'-GATGAGG-5', 2352, 3'-AACTTGG-5', 2382, 3'-AGTGTGG-5', 2418, 3'-GACGTGA-5', 2426, 3'-AACTTAG-5', 2708, 3'-AACTTGG-5', 2717, 3'-GACGTGG-5', 2761, 3'-AACTTGG-5', 3245, 3'-AACGTGA-5', 3289, 3'-GGTCTAG-5', 3488, 3'-GACGAGG-5', 3582, 3'-GGTAAAG-5', 3688, 3'-GACCTGA-5', 3747, 3'-GACTTGG-5', 3784, 3'-GGTATGG-5', 3858, 3'-AGTGTGG-5', 3967, 3'-GGCCTGA-5', 4327, 3'-GACGTGA-5', 4340, 3'-GGTCAAG-5', 4417, 3'-GGTGAGG-5', 4425, 3'-GGTGAAA-5', 4461, 3'-AGTGTAA-5', 4533, 3'-AATTAAG-5', 4542,
  6. complement, negative strand, positive direction is SuccessablesInrc-+.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 16, 3'-GATGAGG-5', 39, 3'-GGCTAGG-5', 45, 3'-AGCTAGG-5', 83, 3'-GACCAGA-5', 109, 3'-AGTGTGA-5', 155, 3'-GGTGAGG-5', 208, 3'-GGCCTGG-5', 240, 3'-GGCCTGG-5', 319, 3'-GACCTGG-5', 348, 3'-AGTGAGG-5', 439, 3'-AGTCTGA-5', 485, 3'-AGTGTGG-5', 527, 3'-GGTGTGA-5', 532, 3'-AATGAGG-5', 657, 3'-GATGAGG-5', 663, 3'-GATTTAG-5', 697,
  7. complement, positive strand, negative direction is SuccessablesInrc+-.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 121, 3'-AACAAGG-5', 71, 3'-GATATGG-5', 77, 3'-GGCAAAG-5', 93, 3'-GGCATGA-5', 124, 3'-GGTATAA-5', 181, 3'-GATGTAA-5', 247, 3'-AACCAGG-5', 262, 3'-AATATGA-5', 274, 3'-AGTGAGA-5', 301, 3'-GACGAAA-5', 312, 3'-GGCCAAG-5', 419, 3'-GGTCAGG-5', 441, 3'-AGCCTGG-5', 459, 3'-AACATAG-5', 468, 3'-AGTGAAA-5', 473, 3'-AGCCTGG-5', 508, 3'-GGCCAAG-5', 556, 3'-GGTCAGG-5', 578, 3'-AATATGG-5', 605, 3'-GGCCAGG-5', 648, 3'-GGCCAAG-5', 692, 3'-GGTCAGG-5', 714, 3'-AGCCTGA-5', 732, 3'-AGCGTGG-5', 741, 3'-GATGTGG-5', 787, 3'-AGCCAAG-5', 874, 3'-AGCCTGG-5', 899, 3'-AGCGAGA-5', 913, 3'-AGCCAGG-5', 948, 3'-GGCATGG-5', 953, 3'-AATCAGG-5', 984, 3'-AACCTGG-5', 1015, 3'-AGTGAGA-5', 1079, 3'-AGCCTGG-5', 1198, 3'-AACATGG-5', 1207, 3'-GGTGAAA-5', 1212, 3'-GGCGTGG-5', 1244, 3'-AACCTAG-5', 1306, 3'-AGTCTGG-5', 1356, 3'-AATAAGA-5', 1365, 3'-AGCAAAA-5', 1371, 3'-AACAAAA-5', 1394, 3'-GGTGTGA-5', 1479, 3'-AACGAAG-5', 1555, 3'-GGCAAAA-5', 1561, 3'-AATGAAA-5', 1582, 3'-AACCTAA-5', 1591, 3'-AATTAAA-5', 1697, 3'-AATATGG-5', 1742, 3'-GGCGTGG-5', 1897, 3'-GGCATGA-5', 1953, 3'-AACCTGG-5', 1959, 3'-AGCCTGG-5', 2009, 3'-AGCAAGA-5', 2023, 3'-AATGTGG-5', 2065, 3'-GGCCAGG-5', 2077, 3'-AGTGTAA-5', 2087, 3'-AGTTTGA-5', 2141, 3'-AACATGG-5', 2152, 3'-GGCGAAA-5', 2157, 3'-GGTCAGG-5', 2250, 3'-AGTTTGA-5', 2257, 3'-AGCCTGG-5', 2268, 3'-AGCATGG-5', 2277, 3'-GGTGAAA-5', 2282, 3'-AACCTGG-5', 2385, 3'-AGCCTGG-5', 2435, 3'-AGTGAGA-5', 2449, 3'-AGCAAAA-5', 2476, 3'-AACAAAA-5', 2490, 3'-AGTAAGA-5', 2503, 3'-GGCCAGG-5', 2519, 3'-GGTCAGG-5', 2587, 3'-AGTGTGG-5', 2605, 3'-AACATGG-5', 2614, 3'-GGTGAAA-5', 2619, 3'-AGTGTGG-5', 2658, 3'-AACCTGG-5', 2720, 3'-AGCCTGG-5', 2770, 3'-AGCATGA-5', 2784, 3'-AACTAAG-5', 2914, 3'-GGCTAAA-5', 3009, 3'-AACTAAG-5', 3031, 3'-GGCGTGG-5', 3047, 3'-AGCCTGG-5', 3128, 3'-AACAAGG-5', 3141, 3'-GGTGAAA-5', 3146, 3'-AACATAA-5', 3169, 3'-GGTGTGG-5', 3186, 3'-AGCCAAG-5', 3273, 3'-AGCCTGG-5', 3298, 3'-AACAAGA-5', 3307, 3'-AGCAAAA-5', 3313, 3'-AACAAGA-5', 3340, 3'-AGCAAGA-5', 3374, 3'-GGCTTGA-5', 3401, 3'-GGCATAG-5', 3446, 3'-AACTAGA-5', 3463, 3'-AACCAGA-5', 3486, 3'-GACAAGA-5', 3759, 3'-GATGTGG-5', 3810, 3'-GACCAGG-5', 3871, 3'-AGTAAGA-5', 3893, 3'-GATGAAA-5', 3922, 3'-GGCCAGG-5', 3951, 3'-AGCCTGG-5', 4037, 3'-AACATAG-5', 4046, 3'-AGTGAGA-5', 4051, 3'-AATGTGA-5', 4092, 3'-GGCCAGG-5', 4102, 3'-GGCATGG-5', 4107, 3'-GGCCAGG-5', 4170, 3'-AGCTTGG-5', 4188, 3'-AGTGAGA-5', 4202, 3'-AGCCAGA-5', 4233, 3'-GACGTGG-5', 4238, 3'-AGCCTGG-5', 4300, 3'-GGTCAAA-5', 4309, 3'-AGCCTGG-5', 4349, 3'-AGTGTGA-5', 4361, 3'-AATGAGG-5', 4557,
  8. complement, positive strand, positive direction is SuccessablesInrc++.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 9, 3'-AGTGTGA-5', 68, 3'-GGTCTGG-5', 111, 3'-GACAAGG-5', 186, 3'-AGTGTGG-5', 385, 3'-AGTAAAA-5', 681, 3'-AGTGAGA-5', 689, 3'-AACTAAA-5', 695, 3'-AATCAAA-5', 700, 3'-GACGTGG-5', 904,
  9. inverse complement, negative strand, negative direction is SuccessablesInrci--.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 32, 3'-GATACAA-5', 213, 3'-GGACCGA-5', 598, 3'-AGTGCGG-5', 664, 3'-GGACTGG-5', 734, 3'-AGTGTGG-5', 882, 3'-GAAGTGA-5', 1056, 3'-AGTGTGG-5', 1128, 3'-GGACCGG-5', 1200, 3'-AGAGCGA-5', 1448, 3'-GGTCCGA-5', 1462, 3'-GATATAG-5', 1528, 3'-AGAACGG-5', 1608, 3'-AAAATAG-5', 1730, 3'-AGTGCAG-5', 1773, 3'-GGACCGA-5', 1843, 3'-AGTGCGG-5', 1992, 3'-AGTGCGG-5', 2208, 3'-AGTGTGG-5', 2418, 3'-AGTACGG-5', 2535, 3'-AGTACGG-5', 2753, 3'-AAAGTAG-5', 2887, 3'-GATTCGA-5', 3033, 3'-GGACCGG-5', 3130, 3'-AGTGCGG-5', 3281, 3'-AGTCCGA-5', 3398, 3'-GGTCTAG-5', 3488, 3'-GGTATGG-5', 3858, 3'-GGTCCGG-5', 3873, 3'-AGTGTGG-5', 3967, 3'-AGTACGG-5', 4118, 3'-GGTCCGA-5', 4255, 3'-AGTGTAA-5', 4533,
  10. inverse complement, negative strand, positive direction is SuccessablesInrci-+.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 18, 3'-GATGCAG-5', 21, 3'-AGTGCAG-5', 26, 3'-GGACCAG-5', 108, 3'-GGAATGA-5', 128, 3'-AGTGTGA-5', 155, 3'-GAAGCGG-5', 231, 3'-AATCCGA-5', 360, 3'-AGAATGA-5', 396, 3'-GAACCAG-5', 401, 3'-AGAGTGA-5', 437, 3'-AGTCTGA-5', 485, 3'-AGTGTGG-5', 527, 3'-GGTGTGA-5', 532, 3'-AGAGTGG-5', 601, 3'-AGAACAG-5', 630, 3'-GAAATGA-5', 655, 3'-GATTTAG-5', 697, 3'-GGAGTGA-5', 911,
  11. inverse complement, positive strand, negative direction is SuccessablesInrci+-.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 100, 3'-AGACTGA-5', 17, 3'-GGACCAG-5', 34, 3'-AAAACAA-5', 69, 3'-GATATGG-5', 77, 3'-AAACTGA-5', 130, 3'-AAAACAG-5', 167, 3'-GGTATAA-5', 181, 3'-GAAACAA-5', 229, 3'-GATGTAA-5', 247, 3'-AGTTCAA-5', 255, 3'-AAACCAG-5', 261, 3'-AATATGA-5', 274, 3'-AGAACAG-5', 288, 3'-AAACTGA-5', 307, 3'-GGTGCGG-5', 380, 3'-AGTGCGA-5', 448, 3'-AATACGA-5', 492, 3'-AAATTAG-5', 499, 3'-AGATTGA-5', 585, 3'-AATATGG-5', 605, 3'-AATACAA-5', 635, 3'-AAATTGG-5', 643, 3'-AGTTCGA-5', 721, 3'-AGACCAG-5', 727, 3'-AATACAA-5', 769, 3'-AAATTAG-5', 777, 3'-GATGTGG-5', 787, 3'-AGAGCGA-5', 911, 3'-GATCCAG-5', 975, 3'-AGATTGG-5', 1045, 3'-AGAGTGA-5', 1077, 3'-AAATTAG-5', 1234, 3'-AGTCTGG-5', 1356, 3'-AGAGCAA-5', 1369, 3'-AAAACAA-5', 1388, 3'-AGTGCAG-5', 1471, 3'-GGTGTGA-5', 1479, 3'-AGTGCAA-5', 1536, 3'-AGAACGA-5', 1553, 3'-AATACAG-5', 1566, 3'-GAAACAA-5', 1585, 3'-GAAATGA-5', 1663, 3'-AAAGCGG-5', 1680, 3'-GAATTAA-5', 1696, 3'-AATATGG-5', 1742, 3'-AATACAA-5', 1878, 3'-AAATTAG-5', 1887, 3'-AGACTGA-5', 1935, 3'-AGAATGG-5', 1948, 3'-AGAGCAA-5', 2021, 3'-AATGTGG-5', 2065, 3'-GGTGCAG-5', 2082, 3'-AGTGTAA-5', 2087, 3'-AGTTTGA-5', 2141, 3'-AGACCAA-5', 2147, 3'-GATACAA-5', 2180, 3'-AAAATGA-5', 2187, 3'-GGTGCGG-5', 2197, 3'-AGTTTGA-5', 2257, 3'-AGACCAG-5', 2263, 3'-AATACAA-5', 2305, 3'-AAACTAG-5', 2313, 3'-AGAGTGA-5', 2447, 3'-GATTCGG-5', 2454, 3'-AAAGCAA-5', 2474, 3'-AAAGCAA-5', 2480, 3'-AAAACAA-5', 2509, 3'-AGACCAG-5', 2600, 3'-AGTGTGG-5', 2605, 3'-AAATCAG-5', 2649, 3'-AGTGTGG-5', 2658, 3'-AAAACAA-5', 2842, 3'-AGAATGG-5', 3004, 3'-AAAATAA-5', 3013, 3'-AAACTAA-5', 3030, 3'-AGACCAG-5', 3123, 3'-AAATTAG-5', 3176, 3'-GGTGTGG-5', 3186, 3'-AGAGCAA-5', 3311, 3'-AAAACAA-5', 3330, 3'-AAATTGA-5', 3358, 3'-GAAGTGA-5', 3410, 3'-GAACTAG-5', 3462, 3'-AAACCAG-5', 3485, 3'-AATCCAG-5', 3681, 3'-GGAACAG-5', 3725, 3'-GGACTGG-5', 3749, 3'-AATGCAG-5', 3772, 3'-GATGTGG-5', 3810, 3'-GGACCAG-5', 3870, 3'-GGAGTAA-5', 3891, 3'-AGTTCAA-5', 4026, 3'-AGACCAG-5', 4032, 3'-AAAATAA-5', 4071, 3'-AATGTGA-5', 4092, 3'-AGTTCAA-5', 4177, 3'-AAAATAA-5', 4221, 3'-AGTGTGA-5', 4361, 3'-AGTCCAA-5', 4502, 3'-GGAATGA-5', 4555,
  12. inverse complement, positive strand, positive direction is SuccessablesInrci++.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 16, 3'-AGTGTGA-5', 68, 3'-GATCCGA-5', 85, 3'-GGTCTGG-5', 111, 3'-AGAGTGG-5', 173, 3'-GGACCGG-5', 242, 3'-AGTGTGG-5', 385, 3'-GAACTGG-5', 579, 3'-AAAATAG-5', 684, 3'-GAACTAA-5', 694, 3'-AAATCAA-5', 699, 3'-GAAACGG-5', 771, 3'-GGACTGG-5', 777, 3'-GGAGTAA-5', 870, 3'-AGTACAG-5', 927, 3'-GGTACGA-5', 933, 3'-AGAACGA-5', 951,
  13. inverse, negative strand, negative direction, is SuccessablesInri--.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 100, 3'-TCTGACT-5', 17, 3'-CCTGGTC-5', 34, 3'-TTTTGTT-5', 69, 3'-CTATACC-5', 77, 3'-TTTGACT-5', 130, 3'-TTTTGTC-5', 167, 3'-CCATATT-5', 181, 3'-CTTTGTT-5', 229, 3'-CTACATT-5', 247, 3'-TCAAGTT-5', 255, 3'-TTTGGTC-5', 261, 3'-TTATACT-5', 274, 3'-TCTTGTC-5', 288, 3'-TTTGACT-5', 307, 3'-CCACGCC-5', 380, 3'-TCACGCT-5', 448, 3'-TTATGCT-5', 492, 3'-TTTAATC-5', 499, 3'-TCTAACT-5', 585, 3'-TTATACC-5', 605, 3'-TTATGTT-5', 635, 3'-TTTAACC-5', 643, 3'-TCAAGCT-5', 721, 3'-TCTGGTC-5', 727, 3'-TTATGTT-5', 769, 3'-TTTAATC-5', 777, 3'-CTACACC-5', 787, 3'-TCTCGCT-5', 911, 3'-CTAGGTC-5', 975, 3'-TCTAACC-5', 1045, 3'-TCTCACT-5', 1077, 3'-TTTAATC-5', 1234, 3'-TCAGACC-5', 1356, 3'-TCTCGTT-5', 1369, 3'-TTTTGTT-5', 1388, 3'-TCACGTC-5', 1471, 3'-CCACACT-5', 1479, 3'-TCACGTT-5', 1536, 3'-TCTTGCT-5', 1553, 3'-TTATGTC-5', 1566, 3'-CTTTGTT-5', 1585, 3'-CTTTACT-5', 1663, 3'-TTTCGCC-5', 1680, 3'-CTTAATT-5', 1696, 3'-TTATACC-5', 1742, 3'-TTATGTT-5', 1878, 3'-TTTAATC-5', 1887, 3'-TCTGACT-5', 1935, 3'-TCTTACC-5', 1948, 3'-TCTCGTT-5', 2021, 3'-TTACACC-5', 2065, 3'-CCACGTC-5', 2082, 3'-TCACATT-5', 2087, 3'-TCAAACT-5', 2141, 3'-TCTGGTT-5', 2147, 3'-CTATGTT-5', 2180, 3'-TTTTACT-5', 2187, 3'-CCACGCC-5', 2197, 3'-TCAAACT-5', 2257, 3'-TCTGGTC-5', 2263, 3'-TTATGTT-5', 2305, 3'-TTTGATC-5', 2313, 3'-TCTCACT-5', 2447, 3'-CTAAGCC-5', 2454, 3'-TTTCGTT-5', 2474, 3'-TTTCGTT-5', 2480, 3'-TTTTGTT-5', 2509, 3'-TCTGGTC-5', 2600, 3'-TCACACC-5', 2605, 3'-TTTAGTC-5', 2649, 3'-TCACACC-5', 2658, 3'-TTTTGTT-5', 2842, 3'-TCTTACC-5', 3004, 3'-TTTTATT-5', 3013, 3'-TTTGATT-5', 3030, 3'-TCTGGTC-5', 3123, 3'-TTTAATC-5', 3176, 3'-CCACACC-5', 3186, 3'-TCTCGTT-5', 3311, 3'-TTTTGTT-5', 3330, 3'-TTTAACT-5', 3358, 3'-CTTCACT-5', 3410, 3'-CTTGATC-5', 3462, 3'-TTTGGTC-5', 3485, 3'-TTAGGTC-5', 3681, 3'-CCTTGTC-5', 3725, 3'-CCTGACC-5', 3749, 3'-TTACGTC-5', 3772, 3'-CTACACC-5', 3810, 3'-CCTGGTC-5', 3870, 3'-CCTCATT-5', 3891, 3'-TCAAGTT-5', 4026, 3'-TCTGGTC-5', 4032, 3'-TTTTATT-5', 4071, 3'-TTACACT-5', 4092, 3'-TCAAGTT-5', 4177, 3'-TTTTATT-5', 4221, 3'-TCACACT-5', 4361, 3'-TCAGGTT-5', 4502, 3'-CCTTACT-5', 4555,
  14. inverse, negative strand, positive direction, is SuccessablesInri-+.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 16, 3'-TCACACT-5', 68, 3'-CTAGGCT-5', 85, 3'-CCAGACC-5', 111, 3'-TCTCACC-5', 173, 3'-CCTGGCC-5', 242, 3'-TCACACC-5', 385, 3'-CTTGACC-5', 579, 3'-TTTTATC-5', 684, 3'-CTTGATT-5', 694, 3'-TTTAGTT-5', 699, 3'-CTTTGCC-5', 771, 3'-CCTGACC-5', 777, 3'-CCTCATT-5', 870, 3'-TCATGTC-5', 927, 3'-CCATGCT-5', 933, 3'-TCTTGCT-5', 951,
  15. inverse, positive strand, negative direction, is SuccessablesInri+-.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 32, 3'-CTATGTT-5', 213, 3'-CCTGGCT-5', 598, 3'-TCACGCC-5', 664, 3'-CCTGACC-5', 734, 3'-TCACACC-5', 882, 3'-CTTCACT-5', 1056, 3'-TCACACC-5', 1128, 3'-CCTGGCC-5', 1200, 3'-TCTCGCT-5', 1448, 3'-CCAGGCT-5', 1462, 3'-CTATATC-5', 1528, 3'-TCTTGCC-5', 1608, 3'-TTTTATC-5', 1730, 3'-TCACGTC-5', 1773, 3'-CCTGGCT-5', 1843, 3'-TCACGCC-5', 1992, 3'-TCACGCC-5', 2208, 3'-TCACACC-5', 2418, 3'-TCATGCC-5', 2535, 3'-TCATGCC-5', 2753, 3'-TTTCATC-5', 2887, 3'-CTAAGCT-5', 3033, 3'-CCTGGCC-5', 3130, 3'-TCACGCC-5', 3281, 3'-TCAGGCT-5', 3398, 3'-CCAGATC-5', 3488, 3'-CCATACC-5', 3858, 3'-CCAGGCC-5', 3873, 3'-TCACACC-5', 3967, 3'-TCATGCC-5', 4118, 3'-CCAGGCT-5', 4255, 3'-TCACATT-5', 4533,
  16. inverse, positive strand, positive direction, is SuccessablesInri++.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 18, 3'-CTACGTC-5', 21, 3'-TCACGTC-5', 26, 3'-CCTGGTC-5', 108, 3'-CCTTACT-5', 128, 3'-TCACACT-5', 155, 3'-CTTCGCC-5', 231, 3'-TTAGGCT-5', 360, 3'-TCTTACT-5', 396, 3'-CTTGGTC-5', 401, 3'-TCTCACT-5', 437, 3'-TCAGACT-5', 485, 3'-TCACACC-5', 527, 3'-CCACACT-5', 532, 3'-TCTCACC-5', 601, 3'-TCTTGTC-5', 630, 3'-CTTTACT-5', 655, 3'-CTAAATC-5', 697, 3'-CCTCACT-5', 911.

Angiotensinogen core promoter elements

[edit | edit source]
Main resources: Gene transcriptions/Elements/Angiotensinogen core promoter and Angiotensinogen core promoter elements

The AGCE1 is supposed to occur before the TSS.[33]

Downstream core elements

[edit | edit source]
Main resources: Gene transcriptions/Elements/Downstream cores and Downstream core elements

The downstream core element (DCE) is a transcription core promoter sequence that is within the transcribed portion of a gene.

The consensus sequence for the DCE is CTTC...CTGT...AGC.[34] These three consensus elements are referred to as subelements: "SI is CTTC, SII is CTGT, and SIII is AGC."[34]

The number of nucleotides between each subelement can apparently vary down to none.

A core promoter that contains all three subelements may be much less common than one containing only one or two.[34] "SI resides approximately from +6 to +11, SII from +16 to +21, and SIII from +30 to +34."[34]

SI as 3'-CTTC-5' can occur as 3 of 4 (CTT, TTC) or 4 of 4 (CTTC). SII as 3'-CTGT-5' can also occur as 3 of 4 (CTG, TGT) or 4 of 4 (CTGT). SIII as AGC is not known to vary.

DCE SIII can function independently of SI and SII.[34]

Downstream promoter elements

[edit | edit source]
Main resources: Gene transcriptions/Downstream promoter elements and Downstream promoter elements
The diagram is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.[1] Credit: Jennifer E.F. Butler & James T. Kadonaga.

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A+1 nucleotide in the Inr"[2]. It is located about 28–33 nucleotides downstream of the transcription start site.[35]

For the Basic programs (starting with SuccessablesDPE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDPE--.bas, looking for 3'-A/G-G-A/T-C/T-A/C/G-5', 163, 3'-GGTCG-5', 35, 3'-AGATA-5', 234, 3'-GGTCC-5', 262, 3'-GGACA-5', 394, 3'-GGTCG-5', 403, 3'-GGTTC-5', 419, 3'-AGTCC-5', 441, 3'-GGACC-5', 459, 3'-AGATG-5', 481, 3'-GGTCG-5', 504, 3'-GGACC-5', 508, 3'-GGTCG-5', 540, 3'-GGTTC-5', 556, 3'-AGTCC-5', 578, 3'-GGACC-5', 596, 3'-AGATG-5', 624, 3'-GGTCC-5', 648, 3'-GGACA-5', 667, 3'-GGTCG-5', 676, 3'-GGTTC-5', 692, 3'-AGTCC-5', 714, 3'-GGTCG-5', 728, 3'-GGTCG-5', 737, 3'-AGATG-5', 758, 3'-GGACA-5', 801, 3'-GGTCG-5', 810, 3'-GGTCC-5', 850, 3'-GGTTC-5', 874, 3'-GGTCG-5', 895, 3'-GGACC-5', 899, 3'-AGACA-5', 919, 3'-GGTCC-5', 948, 3'-GGACA-5', 967, 3'-GGTCG-5', 976, 3'-AGTCC-5', 984, 3'-GGACC-5', 1015, 3'-GGTCG-5', 1061, 3'-AGACA-5', 1085, 3'-GGACA-5', 1131, 3'-GGTCG-5', 1140, 3'-GGTCG-5', 1194, 3'-GGACC-5', 1198, 3'-GGTTG-5', 1203, 3'-AGATG-5', 1224, 3'-GGACA-5', 1258, 3'-GGTCG-5', 1267, 3'-AGTCC-5', 1275, 3'-GGATC-5', 1306, 3'-GGTCA-5', 1352, 3'-AGACC-5', 1356, 3'-AGTTG-5', 1406, 3'-AGACA-5', 1452, 3'-GGTCC-5', 1460, 3'-AGTCG-5', 1486, 3'-AGTTG-5', 1513, 3'-AGATA-5', 1525, 3'-GGTCA-5', 1532, 3'-GGTCG-5', 1611, 3'-AGACA-5', 1776, 3'-GGTCG-5', 1785, 3'-GGTTC-5', 1817, 3'-GGACC-5', 1841, 3'-AGATG-5', 1867, 3'-GGACA-5', 1911, 3'-GGTCG-5', 1920, 3'-GGACC-5', 1959, 3'-GGTCG-5', 2005, 3'-GGACC-5', 2009, 3'-AGACA-5', 2029, 3'-GGTCC-5', 2077, 3'-GGATC-5', 2093, 3'-AGTCC-5', 2134, 3'-GGTTG-5', 2148, 3'-AGATG-5', 2169, 3'-GGTCA-5', 2211, 3'-AGTCC-5', 2250, 3'-GGTCG-5', 2264, 3'-GGACC-5', 2268, 3'-AGATG-5', 2294, 3'-GGACA-5', 2337, 3'-GGTCG-5', 2346, 3'-GGACC-5', 2385, 3'-GGTCG-5', 2431, 3'-GGACC-5', 2435, 3'-AGTTA-5', 2496, 3'-GGTCC-5', 2519, 3'-GGACA-5', 2538, 3'-GGTTG-5', 2547, 3'-AGTCC-5', 2587, 3'-GGTCA-5', 2601, 3'-GGTTG-5', 2610, 3'-AGTCG-5', 2650, 3'-GGTCA-5', 2654, 3'-GGACA-5', 2672, 3'-GGTCG-5', 2681, 3'-GGACC-5', 2720, 3'-GGTCG-5', 2766, 3'-GGACC-5', 2770, 3'-GGTTA-5', 2848, 3'-AGATG-5', 2988, 3'-GGATA-5', 2996, 3'-GGACA-5', 3061, 3'-GGTCG-5', 3070, 3'-AGTCC-5', 3110, 3'-GGTCG-5', 3124, 3'-GGACC-5', 3128, 3'-GGTTG-5', 3137, 3'-AGATG-5', 3158, 3'-GGACA-5', 3200, 3'-AGTCG-5', 3204, 3'-GGTCG-5', 3209, 3'-AGTCC-5', 3217, 3'-GGTCC-5', 3249, 3'-GGTTC-5', 3273, 3'-GGTCG-5', 3294, 3'-GGACC-5', 3298, 3'-AGACA-5', 3319, 3'-AGTCC-5', 3396, 3'-AGTTG-5', 3523, 3'-AGACA-5', 3556, 3'-GGTCC-5', 3564, 3'-GGACG-5', 3579, 3'-GGTCC-5', 3585, 3'-GGTCG-5', 3682, 3'-GGTCG-5', 3701, 3'-AGACG-5', 3706, 3'-GGTCG-5', 3731, 3'-GGACC-5', 3744, 3'-AGACC-5', 3835, 3'-AGTTC-5', 3844, 3'-GGACG-5', 3861, 3'-GGTCC-5', 3871, 3'-GGTCC-5', 3885, 3'-GGACC-5', 3906, 3'-GGTCC-5', 3951, 3'-GGACA-5', 3970, 3'-GGTTG-5', 3979, 3'-GGTTC-5', 4019, 3'-AGTTC-5', 4027, 3'-GGTCG-5', 4033, 3'-GGACC-5', 4037, 3'-AGATG-5', 4062, 3'-GGTCC-5', 4102, 3'-GGACA-5', 4121, 3'-GGTCG-5', 4130, 3'-AGTCC-5', 4138, 3'-GGTCC-5', 4170, 3'-AGTTC-5', 4178, 3'-GGACA-5', 4208, 3'-AGATG-5', 4212, 3'-GGTCC-5', 4253, 3'-GGTCG-5', 4261, 3'-GGACC-5', 4300, 3'-GGTCG-5', 4345, 3'-GGACC-5', 4349, 3'-GGACA-5', 4369, 3'-GGTCA-5', 4415, 3'-AGATG-5', 4430, 3'-AGTCC-5', 4436, 3'-GGTCG-5', 4480, 3'-AGTCG-5', 4489, 3'-GGACC-5', 4494, 3'-GGACC-5', 4546,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDPE-+.bas, looking for 3'-A/G-G-A/T-C/T-A/C/G-5', 18, 3'-GGATG-5', 18, 3'-AGATG-5', 36, 3'-GGTTG-5', 51, 3'-GGACA-5', 91, 3'-GGACC-5', 106, 3'-AGACC-5', 111, 3'-GGATG-5', 135, 3'-GGTCA-5', 381, 3'-AGTCC-5', 424, 3'-AGACA-5', 454, 3'-GGTTC-5', 634, 3'-GGATC-5', 641, 3'-GGATG-5', 660, 3'-AGTTC-5', 761, 3'-GGACA-5', 813, 3'-GGTCA-5', 830, 3'-AGACG-5', 880, 3'-AGACA-5', 893,
  3. positive strand in the negative direction is SuccessablesDPE+-.bas, looking for 3'-A/G-G-A/T-C/T-A/C/G-5', 101, 3'-GGACC-5', 32, 3'-AGATA-5', 57, 3'-GGATA-5', 74, 3'-AGTTG-5', 84, 3'-GGATA-5', 98, 3'-GGATA-5', 108, 3'-AGTCG-5', 157, 3'-AGACA-5', 170, 3'-GGTCA-5', 206, 3'-AGATG-5', 244, 3'-AGTTC-5', 253, 3'-AGACA-5', 422, 3'-GGATC-5', 430, 3'-GGTCA-5', 439, 3'-GGATC-5', 525, 3'-AGACA-5', 559, 3'-GGTCA-5', 568, 3'-GGTCA-5', 576, 3'-AGATC-5', 589, 3'-GGATC-5', 703, 3'-GGTCA-5', 712, 3'-AGTTC-5', 719, 3'-AGACC-5', 725, 3'-GGATG-5', 784, 3'-GGTTG-5', 862, 3'-AGATC-5', 877, 3'-AGATC-5', 972, 3'-GGTTG-5', 1028, 3'-GGACG-5', 1151, 3'-GGATC-5', 1167, 3'-AGTTC-5', 1177, 3'-GGTTG-5', 1319, 3'-AGATG-5', 1438, 3'-AGACA-5', 1569, 3'-AGATA-5', 1595, 3'-GGATC-5', 1812, 3'-AGATG-5', 1828, 3'-AGACC-5', 1834, 3'-AGATC-5', 1987, 3'-GGACA-5', 2117, 3'-AGACC-5', 2121, 3'-AGACC-5', 2145, 3'-AGATA-5', 2177, 3'-GGTTG-5', 2234, 3'-GGATC-5', 2239, 3'-GGTCA-5', 2248, 3'-AGACC-5', 2261, 3'-GGACA-5', 2271, 3'-GGTTG-5', 2398, 3'-AGATC-5', 2413, 3'-AGTCC-5', 2543, 3'-GGATC-5', 2574, 3'-GGTCA-5', 2585, 3'-AGTTG-5', 2592, 3'-AGACC-5', 2598, 3'-AGTTG-5', 2704, 3'-AGTTG-5', 2733, 3'-AGACA-5', 2880, 3'-AGATG-5', 2894, 3'-AGATG-5', 2905, 3'-AGACA-5', 2948, 3'-AGATA-5', 2981, 3'-GGATC-5', 3097, 3'-AGTTG-5', 3115, 3'-AGACC-5', 3121, 3'-GGTTG-5', 3261, 3'-AGATC-5', 3276, 3'-GGACA-5', 3389, 3'-AGACA-5', 3433, 3'-AGATA-5', 3465, 3'-AGATC-5', 3488, 3'-GGTTG-5', 3532, 3'-GGTTG-5', 3605, 3'-AGATG-5', 3620, 3'-AGATG-5', 3627, 3'-GGATA-5', 3655, 3'-GGACA-5', 3756, 3'-AGACC-5', 3761, 3'-GGTTG-5', 3804, 3'-GGTCG-5', 3813, 3'-GGACC-5', 3868, 3'-AGATG-5', 3919, 3'-GGTTG-5', 3945, 3'-GGATC-5', 4006, 3'-AGTTC-5', 4024, 3'-AGACC-5', 4030, 3'-AGTTG-5', 4096, 3'-AGTCC-5', 4126, 3'-GGATC-5', 4157, 3'-AGTTC-5', 4175, 3'-AGACA-5', 4181, 3'-AGACC-5', 4204, 3'-AGACG-5', 4235, 3'-GGATC-5', 4288, 3'-GGTCA-5', 4307, 3'-AGACC-5', 4365, 3'-AGTTC-5', 4417, 3'-GGACA-5', 4468, 3'-AGATC-5', 4475, 3'-AGTCC-5', 4500, 3'-AGACA-5', 4507,
  4. positive strand in the positive direction is SuccessablesDPE++.bas, looking for 3'-A/G-G-A/T-C/T-A/C/G-5', 22, 3'-GGACC-5', 57, 3'-GGTCC-5', 97, 3'-GGACA-5', 178, 3'-GGACA-5', 183, 3'-GGTTG-5', 194, 3'-GGACC-5', 240, 3'-GGTCC-5', 248, 3'-GGTCG-5', 281, 3'-AGTCC-5', 289, 3'-GGACC-5', 319, 3'-AGTCG-5', 336, 3'-GGACC-5', 348, 3'-GGTCA-5', 402, 3'-AGTCC-5', 429, 3'-AGTCG-5', 558, 3'-AGTCG-5', 584, 3'-GGTCC-5', 593, 3'-AGTCG-5', 613, 3'-AGATC-5', 625, 3'-AGATC-5', 637, 3'-GGACG-5', 792, 3'-AGTCA-5', 832,
  5. complement, negative strand, negative direction is SuccessablesDPEc--.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 101, 3'-CCTGG-5', 32, 3'-TCTAT-5', 57, 3'-CCTAT-5', 74, 3'-TCAAC-5', 84, 3'-CCTAT-5', 98, 3'-CCTAT-5', 108, 3'-TCAGC-5', 157, 3'-TCTGT-5', 170, 3'-CCAGT-5', 206, 3'-TCTAC-5', 244, 3'-TCAAG-5', 253, 3'-TCTGT-5', 422, 3'-CCTAG-5', 430, 3'-CCAGT-5', 439, 3'-CCTAG-5', 525, 3'-TCTGT-5', 559, 3'-CCAGT-5', 568, 3'-CCAGT-5', 576, 3'-TCTAG-5', 589, 3'-CCTAG-5', 703, 3'-CCAGT-5', 712, 3'-TCAAG-5', 719, 3'-TCTGG-5', 725, 3'-CCTAC-5', 784, 3'-CCAAC-5', 862, 3'-TCTAG-5', 877, 3'-TCTAG-5', 972, 3'-CCAAC-5', 1028, 3'-CCTGC-5', 1151, 3'-CCTAG-5', 1167, 3'-TCAAG-5', 1177, 3'-CCAAC-5', 1319, 3'-TCTAC-5', 1438, 3'-TCTGT-5', 1569, 3'-TCTAT-5', 1595, 3'-CCTAG-5', 1812, 3'-TCTAC-5', 1828, 3'-TCTGG-5', 1834, 3'-TCTAG-5', 1987, 3'-CCTGT-5', 2117, 3'-TCTGG-5', 2121, 3'-TCTGG-5', 2145, 3'-TCTAT-5', 2177, 3'-CCAAC-5', 2234, 3'-CCTAG-5', 2239, 3'-CCAGT-5', 2248, 3'-TCTGG-5', 2261, 3'-CCTGT-5', 2271, 3'-CCAAC-5', 2398, 3'-TCTAG-5', 2413, 3'-TCAGG-5', 2543, 3'-CCTAG-5', 2574, 3'-CCAGT-5', 2585, 3'-TCAAC-5', 2592, 3'-TCTGG-5', 2598, 3'-TCAAC-5', 2704, 3'-TCAAC-5', 2733, 3'-TCTGT-5', 2880, 3'-TCTAC-5', 2894, 3'-TCTAC-5', 2905, 3'-TCTGT-5', 2948, 3'-TCTAT-5', 2981, 3'-CCTAG-5', 3097, 3'-TCAAC-5', 3115, 3'-TCTGG-5', 3121, 3'-CCAAC-5', 3261, 3'-TCTAG-5', 3276, 3'-CCTGT-5', 3389, 3'-TCTGT-5', 3433, 3'-TCTAT-5', 3465, 3'-TCTAG-5', 3488, 3'-CCAAC-5', 3532, 3'-CCAAC-5', 3605, 3'-TCTAC-5', 3620, 3'-TCTAC-5', 3627, 3'-CCTAT-5', 3655, 3'-CCTGT-5', 3756, 3'-TCTGG-5', 3761, 3'-CCAAC-5', 3804, 3'-CCAGC-5', 3813, 3'-CCTGG-5', 3868, 3'-TCTAC-5', 3919, 3'-CCAAC-5', 3945, 3'-CCTAG-5', 4006, 3'-TCAAG-5', 4024, 3'-TCTGG-5', 4030, 3'-TCAAC-5', 4096, 3'-TCAGG-5', 4126, 3'-CCTAG-5', 4157, 3'-TCAAG-5', 4175, 3'-TCTGT-5', 4181, 3'-TCTGG-5', 4204, 3'-TCTGC-5', 4235, 3'-CCTAG-5', 4288, 3'-CCAGT-5', 4307, 3'-TCTGG-5', 4365, 3'-TCAAG-5', 4417, 3'-CCTGT-5', 4468, 3'-TCTAG-5', 4475, 3'-TCAGG-5', 4500, 3'-TCTGT-5', 4507,
  6. complement, negative strand, positive direction is SuccessablesDPEc-+.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 22, 3'-CCTGG-5', 57, 3'-CCAGG-5', 97, 3'-CCTGT-5', 178, 3'-CCTGT-5', 183, 3'-CCAAC-5', 194, 3'-CCTGG-5', 240, 3'-CCAGG-5', 248, 3'-CCAGC-5', 281, 3'-TCAGG-5', 289, 3'-CCTGG-5', 319, 3'-TCAGC-5', 336, 3'-CCTGG-5', 348, 3'-CCAGT-5', 402, 3'-TCAGG-5', 429, 3'-TCAGC-5', 558, 3'-TCAGC-5', 584, 3'-CCAGG-5', 593, 3'-TCAGC-5', 613, 3'-TCTAG-5', 625, 3'-TCTAG-5', 637, 3'-CCTGC-5', 792, 3'-TCAGT-5', 832,
  7. complement, positive strand, negative direction is SuccessablesDPEc+-.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 101, 3'-GGACC-5', 32, 3'-AGATA-5', 57, 3'-GGATA-5', 74, 3'-AGTTG-5', 84, 3'-GGATA-5', 98, 3'-GGATA-5', 108, 3'-AGTCG-5', 157, 3'-AGACA-5', 170, 3'-GGTCA-5', 206, 3'-AGATG-5', 244, 3'-AGTTC-5', 253, 3'-AGACA-5', 422, 3'-GGATC-5', 430, 3'-GGTCA-5', 439, 3'-GGATC-5', 525, 3'-AGACA-5', 559, 3'-GGTCA-5', 568, 3'-GGTCA-5', 576, 3'-AGATC-5', 589, 3'-GGATC-5', 703, 3'-GGTCA-5', 712, 3'-AGTTC-5', 719, 3'-AGACC-5', 725, 3'-GGATG-5', 784, 3'-GGTTG-5', 862, 3'-AGATC-5', 877, 3'-AGATC-5', 972, 3'-GGTTG-5', 1028, 3'-GGACG-5', 1151, 3'-GGATC-5', 1167, 3'-AGTTC-5', 1177, 3'-GGTTG-5', 1319, 3'-AGATG-5', 1438, 3'-AGACA-5', 1569, 3'-AGATA-5', 1595, 3'-GGATC-5', 1812, 3'-AGATG-5', 1828, 3'-AGACC-5', 1834, 3'-AGATC-5', 1987, 3'-GGACA-5', 2117, 3'-AGACC-5', 2121, 3'-AGACC-5', 2145, 3'-AGATA-5', 2177, 3'-GGTTG-5', 2234, 3'-GGATC-5', 2239, 3'-GGTCA-5', 2248, 3'-AGACC-5', 2261, 3'-GGACA-5', 2271, 3'-GGTTG-5', 2398, 3'-AGATC-5', 2413, 3'-AGTCC-5', 2543, 3'-GGATC-5', 2574, 3'-GGTCA-5', 2585, 3'-AGTTG-5', 2592, 3'-AGACC-5', 2598, 3'-AGTTG-5', 2704, 3'-AGTTG-5', 2733, 3'-AGACA-5', 2880, 3'-AGATG-5', 2894, 3'-AGATG-5', 2905, 3'-AGACA-5', 2948, 3'-AGATA-5', 2981, 3'-GGATC-5', 3097, 3'-AGTTG-5', 3115, 3'-AGACC-5', 3121, 3'-GGTTG-5', 3261, 3'-AGATC-5', 3276, 3'-GGACA-5', 3389, 3'-AGACA-5', 3433, 3'-AGATA-5', 3465, 3'-AGATC-5', 3488, 3'-GGTTG-5', 3532, 3'-GGTTG-5', 3605, 3'-AGATG-5', 3620, 3'-AGATG-5', 3627, 3'-GGATA-5', 3655, 3'-GGACA-5', 3756, 3'-AGACC-5', 3761, 3'-GGTTG-5', 3804, 3'-GGTCG-5', 3813, 3'-GGACC-5', 3868, 3'-AGATG-5', 3919, 3'-GGTTG-5', 3945, 3'-GGATC-5', 4006, 3'-AGTTC-5', 4024, 3'-AGACC-5', 4030, 3'-AGTTG-5', 4096, 3'-AGTCC-5', 4126, 3'-GGATC-5', 4157, 3'-AGTTC-5', 4175, 3'-AGACA-5', 4181, 3'-AGACC-5', 4204, 3'-AGACG-5', 4235, 3'-GGATC-5', 4288, 3'-GGTCA-5', 4307, 3'-AGACC-5', 4365, 3'-AGTTC-5', 4417, 3'-GGACA-5', 4468, 3'-AGATC-5', 4475, 3'-AGTCC-5', 4500, 3'-AGACA-5', 4507,
  8. complement, positive strand, positive direction is SuccessablesDPEc++.bas, looking for 3'-C/T-C-A/T-A/G-T/C/G-5', 22, 3'-GGACC-5', 57, 3'-GGTCC-5', 97, 3'-GGACA-5', 178, 3'-GGACA-5', 183, 3'-GGTTG-5', 194, 3'-GGACC-5', 240, 3'-GGTCC-5', 248, 3'-GGTCG-5', 281, 3'-AGTCC-5', 289, 3'-GGACC-5', 319, 3'-AGTCG-5', 336, 3'-GGACC-5', 348, 3'-GGTCA-5', 402, 3'-AGTCC-5', 429, 3'-AGTCG-5', 558, 3'-AGTCG-5', 584, 3'-GGTCC-5', 593, 3'-AGTCG-5', 613, 3'-AGATC-5', 625, 3'-AGATC-5', 637, 3'-GGACG-5', 792, 3'-AGTCA-5', 832,
  9. inverse complement, negative strand, negative direction is SuccessablesDPEci--.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 174, 3'-TGTCT-5', 13, 3'-TGACT-5', 17, 3'-CAACT-5', 85, 3'-TATCT-5', 100, 3'-CATCC-5', 119, 3'-TGACT-5', 130, 3'-CGACT-5', 140, 3'-TGTCT-5', 168, 3'-GGTCC-5', 262, 3'-CATCT-5', 284, 3'-TGTCT-5', 289, 3'-TGACT-5', 307, 3'-GAACC-5', 328, 3'-TATCT-5', 355, 3'-TGTCC-5', 424, 3'-GGACC-5', 459, 3'-GGACC-5', 508, 3'-TGTCC-5', 561, 3'-CGTCC-5', 565, 3'-TAACT-5', 585, 3'-GGACC-5', 596, 3'-TAACC-5', 643, 3'-GGTCC-5', 648, 3'-CGTCC-5', 697, 3'-GGACT-5', 732, 3'-CGACC-5', 781, 3'-CGACT-5', 825, 3'-CGTCC-5', 831, 3'-GAACT-5', 843, 3'-GGTCC-5', 850, 3'-GGACC-5', 899, 3'-TGTCT-5', 907, 3'-GGTCC-5', 948, 3'-CATCT-5', 970, 3'-CGACT-5', 991, 3'-CGTCC-5', 997, 3'-GAACT-5', 1009, 3'-GGACC-5', 1015, 3'-CGTCT-5', 1023, 3'-TAACC-5', 1045, 3'-TGTCT-5', 1073, 3'-CGACC-5', 1111, 3'-GGACT-5', 1173, 3'-GGACC-5', 1198, 3'-CGACT-5', 1282, 3'-CGTCC-5', 1288, 3'-GAACT-5', 1300, 3'-GATCC-5', 1307, 3'-CGTCT-5', 1314, 3'-GGTCT-5', 1411, 3'-GGTCC-5', 1460, 3'-CGACC-5', 1464, 3'-GGTCT-5', 1518, 3'-TGTCT-5', 1567, 3'-CGTCT-5', 1614, 3'-GGACT-5', 1623, 3'-GAACC-5', 1649, 3'-CATCT-5', 1653, 3'-GGTCT-5', 1670, 3'-TATCT-5', 1710, 3'-CGACC-5', 1746, 3'-CGACC-5', 1756, 3'-CGACT-5', 1800, 3'-CGTCC-5', 1823, 3'-GGACC-5', 1841, 3'-CAACT-5', 1853, 3'-CGACC-5', 1891, 3'-GAACC-5', 1927, 3'-TGACT-5', 1935, 3'-CGTCC-5', 1941, 3'-GGACC-5', 1959, 3'-CGTCT-5', 1967, 3'-GGACC-5', 2009, 3'-TGTCT-5', 2017, 3'-CGACC-5', 2069, 3'-GGTCC-5', 2077, 3'-CGACT-5', 2109, 3'-TGTCT-5', 2119, 3'-GAACT-5', 2127, 3'-CGACT-5', 2226, 3'-CAACC-5', 2235, 3'-GGACC-5', 2268, 3'-CGACC-5', 2326, 3'-CGACT-5', 2361, 3'-CGTCC-5', 2367, 3'-GAACT-5', 2379, 3'-GGACC-5', 2385, 3'-CGTCC-5', 2389, 3'-GGACC-5', 2435, 3'-TGTCT-5', 2443, 3'-TGTCC-5', 2514, 3'-GGTCC-5', 2519, 3'-CGACT-5', 2562, 3'-CGTCC-5', 2568, 3'-GAACT-5', 2580, 3'-CAACT-5', 2593, 3'-TGTCC-5', 2689, 3'-CGACT-5', 2696, 3'-CAACT-5', 2705, 3'-GAACT-5', 2714, 3'-GGACC-5', 2720, 3'-CGACT-5', 2744, 3'-GGACC-5', 2770, 3'-TGTCT-5', 2778, 3'-TGTCT-5', 2878, 3'-TATCT-5', 2903, 3'-GAACC-5', 2921, 3'-CGACC-5', 3035, 3'-CGACC-5', 3041, 3'-CGACT-5', 3085, 3'-GAACT-5', 3103, 3'-CAACC-5', 3116, 3'-GGACC-5', 3128, 3'-CGACC-5', 3180, 3'-CGACT-5', 3224, 3'-GAACT-5', 3242, 3'-GGTCC-5', 3249, 3'-CATCT-5', 3256, 3'-GGACC-5', 3298, 3'-TAACT-5', 3358, 3'-GAACT-5', 3401, 3'-TATCT-5', 3422, 3'-CGTCT-5', 3431, 3'-TATCC-5', 3447, 3'-GATCT-5', 3463, 3'-GGTCT-5', 3486, 3'-CAACT-5', 3505, 3'-TAACC-5', 3529, 3'-CAACT-5', 3533, 3'-TGACT-5', 3542, 3'-GGTCC-5', 3564, 3'-GAACT-5', 3571, 3'-GGTCC-5', 3585, 3'-CGTCT-5', 3589, 3'-CAACC-5', 3606, 3'-CGACT-5', 3649, 3'-TGTCT-5', 3672, 3'-CGACC-5', 3719, 3'-GGACC-5', 3744, 3'-TGACC-5', 3749, 3'-GGACT-5', 3781, 3'-GAACC-5', 3793, 3'-CAACT-5', 3805, 3'-CATCT-5', 3820, 3'-CGACC-5', 3864, 3'-GGTCC-5', 3871, 3'-GGTCC-5', 3885, 3'-GGACC-5', 3906, 3'-TGTCT-5', 3917, 3'-GGACT-5', 3932, 3'-CAACC-5', 3942, 3'-CAACC-5', 3946, 3'-GGTCC-5', 3951, 3'-CGACT-5', 3994, 3'-GAACT-5', 4012, 3'-GGACC-5', 4037, 3'-TATCT-5', 4079, 3'-CAACC-5', 4097, 3'-GGTCC-5', 4102, 3'-CGACT-5', 4145, 3'-GGTCC-5', 4170, 3'-GAACC-5', 4188, 3'-GGTCT-5', 4233, 3'-GGTCC-5', 4253, 3'-GAACC-5', 4268, 3'-CGACT-5', 4276, 3'-CGTCC-5', 4282, 3'-GAACT-5', 4294, 3'-GGACC-5', 4300, 3'-GGACC-5', 4349, 3'-GGTCT-5', 4448, 3'-GGACC-5', 4494, 3'-TGTCT-5', 4518, 3'-GGACC-5', 4546,
  10. inverse complement, negative strand, positive direction is SuccessablesDPEci-+.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 23, 3'-GGACC-5', 106, 3'-TGTCC-5', 138, 3'-GGTCT-5', 169, 3'-TGTCC-5', 180, 3'-CATCC-5', 190, 3'-TGACC-5', 275, 3'-TAACT-5', 294, 3'-GGTCT-5', 332, 3'-TGACC-5', 345, 3'-CGACT-5', 362, 3'-GAACC-5', 399, 3'-GAACC-5', 417, 3'-CAACC-5', 472, 3'-GAACC-5', 498, 3'-TGACC-5', 579, 3'-GAACT-5', 609, 3'-CGTCT-5', 617, 3'-GATCC-5', 642, 3'-CATCC-5', 744, 3'-TGACC-5', 777, 3'-CGACC-5', 919, 3'-TGTCC-5', 928, 3'-GGTCT-5', 941,
  11. inverse complement, positive strand, negative direction is SuccessablesDPEci+-.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 58, 3'-GGACC-5', 32, 3'-TGTCT-5', 479, 3'-CATCC-5', 593, 3'-TAACC-5', 614, 3'-TGACC-5', 734, 3'-CGTCT-5', 754, 3'-GAACC-5', 846, 3'-TGTCT-5', 921, 3'-GATCC-5', 973, 3'-GAACC-5', 1012, 3'-TGACT-5', 1051, 3'-TGTCT-5', 1087, 3'-CGACC-5', 1191, 3'-TGTCT-5', 1222, 3'-GAACC-5', 1303, 3'-CAACC-5', 1407, 3'-GATCT-5', 1482, 3'-CAACC-5', 1514, 3'-TATCC-5', 1529, 3'-CATCC-5', 1572, 3'-GAACT-5', 1685, 3'-TATCT-5', 1731, 3'-CGTCT-5', 1774, 3'-GATCC-5', 1813, 3'-CATCC-5', 1838, 3'-CATCT-5', 1863, 3'-GAACC-5', 1956, 3'-TGTCT-5', 2031, 3'-TGTCT-5', 2165, 3'-TGACC-5', 2189, 3'-CATCT-5', 2290, 3'-GAACC-5', 2382, 3'-GAACC-5', 2717, 3'-TGACT-5', 2786, 3'-CAACC-5', 2844, 3'-CAACT-5', 2911, 3'-TGTCT-5', 2986, 3'-CATCT-5', 3154, 3'-GAACC-5', 3245, 3'-TGTCT-5', 3321, 3'-GAACT-5', 3460, 3'-CAACT-5', 3524, 3'-CATCT-5', 3551, 3'-GGACT-5', 3640, 3'-CGTCC-5', 3698, 3'-GGACT-5', 3747, 3'-GAACC-5', 3784, 3'-TGTCT-5', 3833, 3'-CAACT-5', 3849, 3'-GGACC-5', 3868, 3'-CATCC-5', 3903, 3'-CATCT-5', 4058, 3'-TGTCT-5', 4210, 3'-GGACT-5', 4327, 3'-TGTCT-5', 4371, 3'-GAACC-5', 4451, 3'-CATCC-5', 4456, 3'-GATCC-5', 4476,
  12. inverse complement, positive strand, positive direction is SuccessablesDPEci++.bas, looking for 3'-T/C/G-A/G-A/T-C-C/T-5', 42, 3'-CGTCC-5', 27, 3'-CGTCT-5', 34, 3'-GATCC-5', 45, 3'-GGACC-5', 57, 3'-GATCC-5', 83, 3'-CGACC-5', 87, 3'-GGTCC-5', 97, 3'-GGTCT-5', 109, 3'-TGTCC-5', 132, 3'-CGACT-5', 149, 3'-TGTCC-5', 197, 3'-CGTCC-5', 223, 3'-GGACC-5', 240, 3'-GGTCC-5', 248, 3'-CGTCC-5', 255, 3'-TGACT-5', 296, 3'-CATCC-5', 314, 3'-GGACC-5', 319, 3'-CGTCC-5', 329, 3'-CGACT-5', 339, 3'-GGACC-5', 348, 3'-GGTCT-5', 367, 3'-CGTCT-5', 392, 3'-GGTCT-5', 452, 3'-CGTCT-5', 477, 3'-TGTCC-5', 536, 3'-CGACC-5', 550, 3'-GAACT-5', 577, 3'-GGTCC-5', 593, 3'-CATCT-5', 597, 3'-GATCT-5', 626, 3'-TGTCC-5', 631, 3'-GATCC-5', 638, 3'-TGACT-5', 650, 3'-GAACT-5', 692, 3'-TAACT-5', 722, 3'-CGACC-5', 738, 3'-GGACT-5', 747, 3'-GGACT-5', 775, 3'-GAACC-5', 861, 3'-CGTCT-5', 878, 3'-GGTCT-5', 891,
  13. inverse, negative strand, negative direction, is SuccessablesDPEi--.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 58, 3'-CCTGG-5', 32, 3'-ACAGA-5', 479, 3'-GTAGG-5', 593, 3'-ATTGG-5', 614, 3'-ACTGG-5', 734, 3'-GCAGA-5', 754, 3'-CTTGG-5', 846, 3'-ACAGA-5', 921, 3'-CTAGG-5', 973, 3'-CTTGG-5', 1012, 3'-ACTGA-5', 1051, 3'-ACAGA-5', 1087, 3'-GCTGG-5', 1191, 3'-ACAGA-5', 1222, 3'-CTTGG-5', 1303, 3'-GTTGG-5', 1407, 3'-CTAGA-5', 1482, 3'-GTTGG-5', 1514, 3'-ATAGG-5', 1529, 3'-GTAGG-5', 1572, 3'-CTTGA-5', 1685, 3'-ATAGA-5', 1731, 3'-GCAGA-5', 1774, 3'-CTAGG-5', 1813, 3'-GTAGG-5', 1838, 3'-GTAGA-5', 1863, 3'-CTTGG-5', 1956, 3'-ACAGA-5', 2031, 3'-ACAGA-5', 2165, 3'-ACTGG-5', 2189, 3'-GTAGA-5', 2290, 3'-CTTGG-5', 2382, 3'-CTTGG-5', 2717, 3'-ACTGA-5', 2786, 3'-GTTGG-5', 2844, 3'-GTTGA-5', 2911, 3'-ACAGA-5', 2986, 3'-GTAGA-5', 3154, 3'-CTTGG-5', 3245, 3'-ACAGA-5', 3321, 3'-CTTGA-5', 3460, 3'-GTTGA-5', 3524, 3'-GTAGA-5', 3551, 3'-CCTGA-5', 3640, 3'-GCAGG-5', 3698, 3'-CCTGA-5', 3747, 3'-CTTGG-5', 3784, 3'-ACAGA-5', 3833, 3'-GTTGA-5', 3849, 3'-CCTGG-5', 3868, 3'-GTAGG-5', 3903, 3'-GTAGA-5', 4058, 3'-ACAGA-5', 4210, 3'-CCTGA-5', 4327, 3'-ACAGA-5', 4371, 3'-CTTGG-5', 4451, 3'-GTAGG-5', 4456, 3'-CTAGG-5', 4476,
  14. inverse, negative strand, positive direction, is SuccessablesDPEi-+.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 42, 3'-GCAGG-5', 27, 3'-GCAGA-5', 34, 3'-CTAGG-5', 45, 3'-CCTGG-5', 57, 3'-CTAGG-5', 83, 3'-GCTGG-5', 87, 3'-CCAGG-5', 97, 3'-CCAGA-5', 109, 3'-ACAGG-5', 132, 3'-GCTGA-5', 149, 3'-ACAGG-5', 197, 3'-GCAGG-5', 223, 3'-CCTGG-5', 240, 3'-CCAGG-5', 248, 3'-GCAGG-5', 255, 3'-ACTGA-5', 296, 3'-GTAGG-5', 314, 3'-CCTGG-5', 319, 3'-GCAGG-5', 329, 3'-GCTGA-5', 339, 3'-CCTGG-5', 348, 3'-CCAGA-5', 367, 3'-GCAGA-5', 392, 3'-CCAGA-5', 452, 3'-GCAGA-5', 477, 3'-ACAGG-5', 536, 3'-GCTGG-5', 550, 3'-CTTGA-5', 577, 3'-CCAGG-5', 593, 3'-GTAGA-5', 597, 3'-CTAGA-5', 626, 3'-ACAGG-5', 631, 3'-CTAGG-5', 638, 3'-ACTGA-5', 650, 3'-CTTGA-5', 692, 3'-ATTGA-5', 722, 3'-GCTGG-5', 738, 3'-CCTGA-5', 747, 3'-CCTGA-5', 775, 3'-CTTGG-5', 861, 3'-GCAGA-5', 878, 3'-CCAGA-5', 891,
  15. inverse, positive strand, negative direction, is SuccessablesDPEi+-.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 174, 3'-ACAGA-5', 13, 3'-ACTGA-5', 17, 3'-GTTGA-5', 85, 3'-ATAGA-5', 100, 3'-GTAGG-5', 119, 3'-ACTGA-5', 130, 3'-GCTGA-5', 140, 3'-ACAGA-5', 168, 3'-CCAGG-5', 262, 3'-GTAGA-5', 284, 3'-ACAGA-5', 289, 3'-ACTGA-5', 307, 3'-CTTGG-5', 328, 3'-ATAGA-5', 355, 3'-ACAGG-5', 424, 3'-CCTGG-5', 459, 3'-CCTGG-5', 508, 3'-ACAGG-5', 561, 3'-GCAGG-5', 565, 3'-ATTGA-5', 585, 3'-CCTGG-5', 596, 3'-ATTGG-5', 643, 3'-CCAGG-5', 648, 3'-GCAGG-5', 697, 3'-CCTGA-5', 732, 3'-GCTGG-5', 781, 3'-GCTGA-5', 825, 3'-GCAGG-5', 831, 3'-CTTGA-5', 843, 3'-CCAGG-5', 850, 3'-CCTGG-5', 899, 3'-ACAGA-5', 907, 3'-CCAGG-5', 948, 3'-GTAGA-5', 970, 3'-GCTGA-5', 991, 3'-GCAGG-5', 997, 3'-CTTGA-5', 1009, 3'-CCTGG-5', 1015, 3'-GCAGA-5', 1023, 3'-ATTGG-5', 1045, 3'-ACAGA-5', 1073, 3'-GCTGG-5', 1111, 3'-CCTGA-5', 1173, 3'-CCTGG-5', 1198, 3'-GCTGA-5', 1282, 3'-GCAGG-5', 1288, 3'-CTTGA-5', 1300, 3'-CTAGG-5', 1307, 3'-GCAGA-5', 1314, 3'-CCAGA-5', 1411, 3'-CCAGG-5', 1460, 3'-GCTGG-5', 1464, 3'-CCAGA-5', 1518, 3'-ACAGA-5', 1567, 3'-GCAGA-5', 1614, 3'-CCTGA-5', 1623, 3'-CTTGG-5', 1649, 3'-GTAGA-5', 1653, 3'-CCAGA-5', 1670, 3'-ATAGA-5', 1710, 3'-GCTGG-5', 1746, 3'-GCTGG-5', 1756, 3'-GCTGA-5', 1800, 3'-GCAGG-5', 1823, 3'-CCTGG-5', 1841, 3'-GTTGA-5', 1853, 3'-GCTGG-5', 1891, 3'-CTTGG-5', 1927, 3'-ACTGA-5', 1935, 3'-GCAGG-5', 1941, 3'-CCTGG-5', 1959, 3'-GCAGA-5', 1967, 3'-CCTGG-5', 2009, 3'-ACAGA-5', 2017, 3'-GCTGG-5', 2069, 3'-CCAGG-5', 2077, 3'-GCTGA-5', 2109, 3'-ACAGA-5', 2119, 3'-CTTGA-5', 2127, 3'-GCTGA-5', 2226, 3'-GTTGG-5', 2235, 3'-CCTGG-5', 2268, 3'-GCTGG-5', 2326, 3'-GCTGA-5', 2361, 3'-GCAGG-5', 2367, 3'-CTTGA-5', 2379, 3'-CCTGG-5', 2385, 3'-GCAGG-5', 2389, 3'-CCTGG-5', 2435, 3'-ACAGA-5', 2443, 3'-ACAGG-5', 2514, 3'-CCAGG-5', 2519, 3'-GCTGA-5', 2562, 3'-GCAGG-5', 2568, 3'-CTTGA-5', 2580, 3'-GTTGA-5', 2593, 3'-ACAGG-5', 2689, 3'-GCTGA-5', 2696, 3'-GTTGA-5', 2705, 3'-CTTGA-5', 2714, 3'-CCTGG-5', 2720, 3'-GCTGA-5', 2744, 3'-CCTGG-5', 2770, 3'-ACAGA-5', 2778, 3'-ACAGA-5', 2878, 3'-ATAGA-5', 2903, 3'-CTTGG-5', 2921, 3'-GCTGG-5', 3035, 3'-GCTGG-5', 3041, 3'-GCTGA-5', 3085, 3'-CTTGA-5', 3103, 3'-GTTGG-5', 3116, 3'-CCTGG-5', 3128, 3'-GCTGG-5', 3180, 3'-GCTGA-5', 3224, 3'-CTTGA-5', 3242, 3'-CCAGG-5', 3249, 3'-GTAGA-5', 3256, 3'-CCTGG-5', 3298, 3'-ATTGA-5', 3358, 3'-CTTGA-5', 3401, 3'-ATAGA-5', 3422, 3'-GCAGA-5', 3431, 3'-ATAGG-5', 3447, 3'-CTAGA-5', 3463, 3'-CCAGA-5', 3486, 3'-GTTGA-5', 3505, 3'-ATTGG-5', 3529, 3'-GTTGA-5', 3533, 3'-ACTGA-5', 3542, 3'-CCAGG-5', 3564, 3'-CTTGA-5', 3571, 3'-CCAGG-5', 3585, 3'-GCAGA-5', 3589, 3'-GTTGG-5', 3606, 3'-GCTGA-5', 3649, 3'-ACAGA-5', 3672, 3'-GCTGG-5', 3719, 3'-CCTGG-5', 3744, 3'-ACTGG-5', 3749, 3'-CCTGA-5', 3781, 3'-CTTGG-5', 3793, 3'-GTTGA-5', 3805, 3'-GTAGA-5', 3820, 3'-GCTGG-5', 3864, 3'-CCAGG-5', 3871, 3'-CCAGG-5', 3885, 3'-CCTGG-5', 3906, 3'-ACAGA-5', 3917, 3'-CCTGA-5', 3932, 3'-GTTGG-5', 3942, 3'-GTTGG-5', 3946, 3'-CCAGG-5', 3951, 3'-GCTGA-5', 3994, 3'-CTTGA-5', 4012, 3'-CCTGG-5', 4037, 3'-ATAGA-5', 4079, 3'-GTTGG-5', 4097, 3'-CCAGG-5', 4102, 3'-GCTGA-5', 4145, 3'-CCAGG-5', 4170, 3'-CTTGG-5', 4188, 3'-CCAGA-5', 4233, 3'-CCAGG-5', 4253, 3'-CTTGG-5', 4268, 3'-GCTGA-5', 4276, 3'-GCAGG-5', 4282, 3'-CTTGA-5', 4294, 3'-CCTGG-5', 4300, 3'-CCTGG-5', 4349, 3'-CCAGA-5', 4448, 3'-CCTGG-5', 4494, 3'-ACAGA-5', 4518, 3'-CCTGG-5', 4546,
  16. inverse, positive strand, positive direction, is SuccessablesDPEi++.bas, looking for 3'-A/C/G-C/T-A/T-G-A/G-5', 23, 3'-CCTGG-5', 106, 3'-ACAGG-5', 138, 3'-CCAGA-5', 169, 3'-ACAGG-5', 180, 3'-GTAGG-5', 190, 3'-ACTGG-5', 275, 3'-ATTGA-5', 294, 3'-CCAGA-5', 332, 3'-ACTGG-5', 345, 3'-GCTGA-5', 362, 3'-CTTGG-5', 399, 3'-CTTGG-5', 417, 3'-GTTGG-5', 472, 3'-CTTGG-5', 498, 3'-ACTGG-5', 579, 3'-CTTGA-5', 609, 3'-GCAGA-5', 617, 3'-CTAGG-5', 642, 3'-GTAGG-5', 744, 3'-ACTGG-5', 777, 3'-GCTGG-5', 919, 3'-ACAGG-5', 928, 3'-CCAGA-5', 941.

See also

[edit | edit source]

References

[edit | edit source]
  1. ↑ 1.0 1.1 Jennifer E.F. Butler, James T. Kadonaga (October 15, 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development 16 (20): 2583–292. doi:10.1101/gad.1026202. PMID 12381658. http://genesdev.cshlp.org/content/16/20/2583.full. 
  2. ↑ 2.0 2.1 2.2 2.3 Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter". Annual Review of Biochemistry 72 (1): 449-79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. http://www.lps.ens.fr/~monasson/Houches/Kadonaga/CorePromoterAnnuRev2003.pdf. Retrieved 2012-05-07. 
  3. ↑ 3.0 3.1 Gillian E. Chalkley and C. Peter Verrijzer (September 1, 1999). "DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator". The EMBO Journal 18 (17): 4835-45. PMID 10469661. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171555/pdf/004835.pdf. Retrieved 2012-04-26. 
  4. ↑ S. T. Smale (1997). "Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes". Biochim. Biophys. Acta. 1351: 73-88. 
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Chuhu Yang, Eugene Bolotin, Tao Jiang, Frances M. Sladek, Ernest Martinez. (March 7, 2007). "Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene 389 (1): 52-65. doi:10.1016/j.gene.2006.09.029. PMID 17123746. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955227/?tool=pubmed. 
  6. ↑ Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proc Natl Acad Sci USA 103 (5): 1412–1417. doi:10.1073/pnas.0510310103. PMID 16432200. PMC 1345710. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1345710/. 
  7. ↑ Alan K. Kutach, James T. Kadonaga (July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology 20 (13): 4754-64. PMID 10848601. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC85905/pdf/mb004754.pdf. Retrieved 2012-07-15. 
  8. ↑ Tianbao Yang and B. W. Poovaiah (22 November 2002). "A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants". Journal of Biological Chemistry 277 (47): 45049-45058. doi:10.1074/jbc.M207941200. http://www.jbc.org/content/277/47/45049.full. Retrieved 2017-02-05. 
  9. ↑ Cornelis Murre and David Baltimore (1992). The Helix-Loop-Helix Motif: Structure and Function, In: Transcriptional Regulation. 22B. Cold Spring Harbor Laboratory Press. pp. 861-79. doi:10.1101/087969425.22B.861. https://cshmonographs.org/csh/index.php/monographs/article/viewPDFInterstitial/3449/2723. Retrieved 2017-02-08. 
  10. ↑ 10.0 10.1 Mary Lynch, Li Chen, Michael J. Ravitz, Sapna Mehtani, Kevin Korenblat, Michael J. Pazin and Emmett V. Schmidt (August 2005). "hnRNP K Binds a Core Polypyrimidine Element in the Eukaryotic Translation Initiation Factor 4E (eIF4E) Promoter, and Its Regulation of eIF4E Contributes to Neoplastic Transformation". Molecular and Cellular Biology 25 (15): 6436-53. doi:10.1128/MCB.25.15.6436-6453.2005. http://mcb.asm.org/content/25/15/6436.full. Retrieved 2013-03-17. 
  11. ↑ 11.0 11.1 11.2 Montaña Mena, Francisco Javier Cejudo, Ines Isabel-Lamoneda and Pilar Carbonero (1 September 2002). "A Role for the DOF Transcription Factor BPBF in the Regulation of Gibberellin-Responsive Genes in Barley Aleurone". Plant Physiology 130 (1): 111-9. doi:10.1104/pp.005561. http://www.plantphysiol.org/content/130/1/111.full. Retrieved 2017-02-19. 
  12. ↑ K Oeda, J Salinas, and N H Chua (July 1991). "A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes". The EMBO Journal 10 (7): 1793–1802. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC452853/. Retrieved 2017-02-13. 
  13. ↑ H Imataka, K Sogawa, KI Yasumoto, Y Kikuchi, K Sasano, A Kobayashi, M Hayami, and Y Fujii-Kuriyama (October 1992). "Two regulatory proteins that bind to the basic transcription element (BTE), a GC box sequence in the promoter region of the rat P-4501A1 gene". The EMBO Journal 11 (10): 3663-71. PMID 1356762. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC556826/pdf/emboj00095-0180.pdf. Retrieved 2013-01-27. 
  14. ↑ Ute Fischer and Wolfgang Dröge-Laser (2004). "Overexpression of NtERF5, a New Member of the Tobacco Ethylene Response Transcription Factor Family Enhances Resistance to Tobacco mosaic virus". Molecular Plant-Microbe Interactions 17 (10): 1162-71. http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI.2004.17.10.1162. Retrieved 2017-04-05. 
  15. ↑ 15.0 15.1 15.2 Montaña Mena, Jesus Vicente-Carbajosa, Robert J. Schmidt and Pilar Carbonero (October 1998). "An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm". The Plant Journal 16 (1): 53-62. doi:10.1046/j.1365-313x.1998.00275.x. http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.1998.00275.x/full. Retrieved 2017-02-19. 
  16. ↑ Timofey S. Rozhdestvensky, Thean Hock Tang, Inna V. Tchirkova, Jürgen Brosius, Jean‐Pierre Bachellerie and Alexander Hüttenhofer (2003). "Binding of L7Ae protein to the K‐turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Research 31 (3): 869-77. doi:10.1093/nar/gkg175. http://nar.oxfordjournals.org/content/31/3/869.long. Retrieved 2014-06-08. 
  17. ↑ Vincent Laudet, Dominique Stehelin and Hans Clevers (1993). "Ancestry and diversity of the HMG box superfamily". Nucleic Acids Research 21 (10): 2493-501. https://academic.oup.com/nar/article-pdf/21/10/2493/4086740/21-10-2493.pdf. Retrieved 2017-04-05. 
  18. ↑ 18.0 18.1 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (January 1983). "The tac promoter: A functional hybrid derived from the trpand lac promoters". Proceedings of the National Academy of Sciences USA 80 (1): 21-5. http://www.pnas.org/content/80/1/21.full.pdf. Retrieved 2017-02-19. 
  19. ↑ Wangjie Yu and Paul E. Hardin (2006). "Circadian oscillators of Drosophila and mammals". Journal of Cell Science 119: 4793-5. doi:10.1242/jcs.03174. http://jcs.biologists.org/content/119/23/4793.short. Retrieved 2017-02-19. 
  20. ↑ Alan C. Christensen & Elton T. Young (23 September 1982). "T4 late transcripts are initiated near a conserved DNA sequence". Nature 299 (5881): 369-71. doi:10.1038/299369a0. http://www.nature.com/nature/journal/v299/n5881/abs/299369a0.html. Retrieved 2017-02-19. 
  21. ↑ Claudio W. Pikielny, John L. Teem, Michael Rosbash (September 1983). "Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing". Cell 34 (2): 395-403. doi:10.1016/0092-8674(83)90373-2. https://pdfs.semanticscholar.org/82a1/d2fb5feabbfc7a64e0b3d84be536c7a4110d.pdf. Retrieved 2017-04-05. 
  22. ↑ Francisco Rivero (June 2002). "mRNA processing in Dictyostelium: sequence requirements for termination and splicing". Protist 153 (2): 169-76. doi:10.1078/1434-4610-00095. http://www.academia.edu/download/45750040/1434-4610-0009520160518-7945-1y17rxg.pdf. Retrieved 2017-04-05. 
  23. ↑ 23.0 23.1 XIAN-YANG ZHANG, NABILA JABRANE-FERRAT, CLEMENT K. ASIEDU, SANJA SAMAC, B. MATIJA PETERLIN, AND MELANIE EHRLICH (November 1993). "The Major Histocompatibility Complex Class II Promoter-Binding Protein RFX (NF-X) Is a Methylated DNA-Binding Protein". MOLECULAR AND CELLULAR BIOLOGY 13 (11): 6810-8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC364743/pdf/molcellb00023-0210.pdf. Retrieved 2017-04-05. 
  24. ↑ Koji Koike, Takeshi Uchiumi, Takefumi Ohga, Satoshi Toh, Morimasa Wada, Kimitoshi Kohno, and Michihiko Kuwano (17 November 1997). "Nuclear translocation of the Y-box binding protein by ultraviolet irradiation". FEBS Letters 417 (3): 390-4. doi:10.1016/S0014-5793(97)01296-9. http://onlinelibrary.wiley.com/doi/10.1016/S0014-5793(97)01296-9/full. Retrieved 2017-04-05. 
  25. ↑ Lifton RP, Goldberg ML, Karp RW, Hogness DS (1978). "The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications". Cold Spring Harb Symp Quant Biol 42: 1047–51. PMID 98262. 
  26. ↑ 26.0 26.1 Wensheng Deng, Stefan G.E. Roberts (October 15, 2005). "A core promoter element downstream of the TATA box that is recognized by TFIIB". Genes & Development 19 (20): 2418–23. doi:10.1101/gad.342405. PMID 16230532. http://genesdev.cshlp.org/content/19/20/2418.full. 
  27. ↑ Yumiko Tokusumi, Ying Ma, Xianzhou Song, Raymond H. Jacobson, and Shinako Takada (March 2007). "The New Core Promoter Element XCPE1 (X Core Promoter Element 1) Directs Activator-, Mediator-, and TATA-Binding Protein-Dependent but TFIID-Independent RNA Polymerase II Transcription from TATA-Less Promoters". Molecular and Cellular Biology 27 (5): 1844-58. doi:10.1128/MCB.01363-06. PMID 17210644. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820453/. Retrieved 2013-02-09. 
  28. ↑ Chin Yan Lim, Buyung Santoso, Thomas Boulay, Emily Dong, Uwe Ohler, and James T. Kadonaga (July 1, 2004). "The MTE, a new core promoter element for transcription by RNA polymerase II". Genes & Development 18 (13): 1606-17. doi:10.1101/gad.1193404. PMID 15231738. http://genesdev.cshlp.org/content/18/13/1606.full. Retrieved 2013-02-10. 
  29. ↑ Upinder Singh, Joshua B. Rogers (August 21, 1998). "The Novel Core Promoter Element GAAC in the hgl5 Gene of Entamoeba histolytica Is Able to Direct a Transcription Start Site Independent of TATA or Initiator Regions". The Journal of Biological Chemistry 273 (34): 21663-8. doi:10.1074/jbc.273.34.21663. http://www.jbc.org/content/273/34/21663.full. Retrieved 2013-02-13. 
  30. ↑ J. Carcamo, L. Buckbinder and D. Reinberg (1991). "The initiator directs the assembly of a transcription factor IID-dependent transcription complex". Proceedings of the National Academy of Sciences USA 88: 8052-6. 
  31. ↑ L. Weis and D. Reinberg (1997). "Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding protein associated factors and initiator-binding proteins". Mol. Cell. Biol. 17: 2973-84. 
  32. ↑ 32.0 32.1 Tamar Juven-Gershon, Jer-Yuan Hsu, Joshua W. M. Theisen, and James T. Kadonaga (June 2008). "The RNA Polymerase II Core Promoter – the Gateway to Transcription". Current Opinion in Cell Biology 20 (3): 253-9. doi:10.1016/j.ceb.2008.03.003. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586601/. Retrieved 2013-02-13. 
  33. ↑ Noriyuki Sato; Tomohiro Katsuya; Hiromi Rakugi; Seiju Takami; Yukiko Nakata; Tetsuro Miki; Jitsuo Higaki; Toshio Ogihara (September 1997). "Association of Variants in Critical Core Promoter Element of Angiotensinogen Gene With Increased Risk of Essential Hypertension in Japanese". Hypertension 30 (3 Pt 1): 321-5. doi:10.1161/01.HYP.30.3.321. PMID 9314411. http://www.ncbi.nlm.nih.gov/pubmed/9314411. Retrieved 2012-02-20. 
  34. ↑ 34.0 34.1 34.2 34.3 34.4 Dong-Hoon Lee, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg and Brian A. Lewis (November 2005). "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1". Molecular and Cellular Biology 25 (21): 9674-86. doi:10.1128/MCB.25.21.9674-9686.2005. PMID 16227614. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1265815/. Retrieved 2010-10-23. 
  35. ↑ Tamar Juven-Gershon and James T. Kadonaga (15 March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology 339 (2): 225-9. doi:10.1016/j.ydbio.2009.08.009. http://www.sciencedirect.com/science/article/pii/S0012160609011166. Retrieved 2016-01-16. 
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