Activating protein gene transcriptions

Jump to navigation Jump to search

Associate Editor(s)-in-Chief: Henry A. Hoff

Activating Protein 2 (AP-2) is a family of closely related transcription factors[1][2] which plays a critical role in regulating gene expression during early development.[3]

Human genes

Main article: Human genes

Gene ID: 7020 is TFAP2A transcription factor AP-2 alpha on 6p24.3: "The protein encoded by this gene is a transcription factor that binds the consensus sequence 5'-GCCNNNGGC-3'. The encoded protein functions as either a homodimer or as a heterodimer with similar family members. This protein activates the transcription of some genes while inhibiting the transcription of others. Defects in this gene are a cause of branchiooculofacial syndrome (BOFS). Three transcript variants encoding different isoforms have been found for this gene."[4]

  1. NP_001027451.1 transcription factor AP-2-alpha isoform b: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a."[4]
  2. NP_001035890.1 transcription factor AP-2-alpha isoform c: "Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a."[4]
  3. NP_001358995.1 transcription factor AP-2-alpha, variant 1.[4]

Gene ID: 7021 is TFAP2B transcription factor AP-2 beta on 6p12.3: "This gene encodes a member of the AP-2 family of transcription factors. AP-2 proteins form homo- or hetero-dimers with other AP-2 family members and bind specific DNA sequences. They are thought to stimulate cell proliferation and suppress terminal differentiation of specific cell types during embryonic development. Specific AP-2 family members differ in their expression patterns and binding affinity for different promoters. This protein functions as both a transcriptional activator and repressor. Mutations in this gene result in autosomal dominant Char syndrome, suggesting that this gene functions in the differentiation of neural crest cell derivatives."[5]

Gene ID: 7022 is TFAP2C transcription factor AP-2 gamma on 20q13.31: "The protein encoded by this gene is a sequence-specific DNA-binding transcription factor involved in the activation of several developmental genes. The encoded protein can act as either a homodimer or heterodimer with other family members and is induced during retinoic acid-mediated differentiation. It plays a role in the development of the eyes, face, body wall, limbs, and neural tube."[6]

Gene ID: 83741 is TFAP2D transcription factor AP-2 delta on 6p12.3.[7]

Gene ID: 339488 is TFAP2E transcription factor AP-2 epsilon on 1p34.3 aka AP2E.[8]

AP-2 alpha consensus sequences

"The protein encoded by this gene is a transcription factor that binds the consensus sequence 5'-GCCNNNGGC-3'."[4] Note that consensus sequence GCCNNNGGC is included in the analysis of (C/G)CCNNNGG(C/G)[9].

Two activating protein response elements have been investigated: [G/C]CCN(3,4)GG[G/C] and GCCCACGGG.[9]

  1. Negative strand, negative direction: 0.
  2. Positive strand, negative direction: 0.
  3. Negative strand, positive direction: 5, GCCCTGGGC at 3498, GCCTCTGGC at 2884, GCCACCGGC at 1547, GCCACCGGC at 1295, GCCAGCGGC at 332.
  4. positive strand, positive direction: 1, GCCCCCGGC at 1647.

AP-2 alpha positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GCCCTGGGC at 3498, GCCTCTGGC at 2884, GCCACCGGC at 1547, GCCACCGGC at 1295, GCCAGCGGC at 332.
  2. Positive strand, positive direction: GCCCCCGGC at 1647.

AP-2 alpha random dataset samplings

  1. AP2ar0: 2, GCCGGTGGC at 4263, GCCGCAGGC at 3245.
  2. AP2ar1: 2, GCCCCCGGC at 720, GCCAGGGGC at 670.
  3. AP2ar2: 1, GCCAGGGGC at 2282.
  4. AP2ar3: 2, GCCCGGGGC at 3403, GCCGCCGGC at 1455.
  5. AP2ar4: 3, GCCTTGGGC at 3547, GCCCCTGGC at 3232, GCCGCCGGC at 1025.
  6. AP2ar5: 7, GCCCAGGGC at 4370, GCCAGCGGC at 685, GCCCTTGGC at 355.
  7. AP2ar6: 1, GCCCCAGGC at 685.
  8. AP2ar7: 0.
  9. AP2ar8: 3, GCCGGGGGC at 3319, GCCCACGGC at 944, GCCAACGGC at 131.
  10. AP2ar9: 5, GCCCGTGGC at 2944, GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

AP2ar arbitrary (evens) (4560-2846) UTRs

  1. AP2ar0: GCCGGTGGC at 4263, GCCGCAGGC at 3245.
  2. AP2ar4: GCCTTGGGC at 3547, GCCCCTGGC at 3232.
  3. AP2ar8: GCCGGGGGC at 3319.

AP2ar alternate (odds) (4560-2846) UTRs

  1. AP2ar3: GCCCGGGGC at 3403.
  2. AP2ar5: GCCCAGGGC at 4370.
  3. AP2ar9: GCCCGTGGC at 2944.

AP2ar arbitrary positive direction (odds) (4445-4265) core promoters

  1. AP2ar5: GCCCAGGGC at 4370.

AP2ar alternate positive direction (evens) (4265-4050) proximal promoters

  1. AP2ar0: GCCGGTGGC at 4263.

AP2ar arbitrary negative direction (evens) (2596-1) distal promoters

  1. AP2ar2: GCCAGGGGC at 2282.
  2. AP2ar4: GCCGCCGGC at 1025.
  3. AP2ar6: GCCCCAGGC at 685.
  4. AP2ar8: GCCCACGGC at 944, GCCAACGGC at 131.

AP2ar alternate negative direction (odds) (2596-1) distal promoters

  1. AP2ar1: GCCCCCGGC at 720, GCCAGGGGC at 670.
  2. AP2ar3: GCCGCCGGC at 1455.
  3. AP2ar5: GCCAGCGGC at 685, GCCCTTGGC at 355.
  4. AP2ar9: GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

AP2ar arbitrary positive direction (odds) (4050-1) distal promoters

  1. AP2ar1: GCCCCCGGC at 720, GCCAGGGGC at 670.
  2. AP2ar3: GCCCGGGGC at 3403, GCCGCCGGC at 1455.
  3. AP2ar5: GCCAGCGGC at 685, GCCCTTGGC at 355.
  4. AP2ar9: GCCCGTGGC at 2944, GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

AP2ar alternate positive direction (evens) (4050-1) distal promoters

  1. AP2ar0: GCCGCAGGC at 3245.
  2. AP2ar2: GCCAGGGGC at 2282.
  3. AP2ar4: GCCTTGGGC at 3547, GCCCCTGGC at 3232, GCCGCCGGC at 1025.
  4. AP2ar6: GCCCCAGGC at 685.
  5. AP2ar8: GCCGGGGGC at 3319, GCCCACGGC at 944, GCCAACGGC at 131.

AP-2 alpha analysis and results

Main article: Complex locus A1BG and ZNF497 § AP2as

"The protein encoded by this gene is a transcription factor that binds the consensus sequence 5'-GCCNNNGGC-3'."[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 5 10 0.5 0.4
Randoms UTR alternate negative 3 10 0.3 0.4
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 5 10 0.5 0.7
Randoms Distal alternate negative 9 10 0.9 0.7
Reals Distal positive 6 2 3 3 ± 2 (-+5,++1)
Randoms Distal arbitrary positive 11 10 1.1 1.0
Randoms Distal alternate positive 9 10 0.9 1.0

Comparison:

The occurrences of real AP2as in the positive direction on the negative strand are greater than the randoms, the AP2a in the positive direction on the positive strand is within the range of the randoms. This suggests that the real AP2as are likely active or activable.

Consensus sequences

Main article: Consensus sequence gene transcriptions

"AP-2 proteins can bind to G/C-rich elements, such as 5’-[G/C]CCN(3,4)GG[G/C]-3’ (41, 42)."[9]

Consensus sequences for the Activating protein 2 (AP-2) are GCCTGGCC.[10]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Activating protein elements in either promoter.
  2. A1BG is not transcribed by an Activating protein elements.
  3. Activating protein elements do not participate in the transcription of A1BG.

AP-1s

"A conserved AP-1 (TGAGTCA) site was identified in the gpnmb promoter as well as a conserved core-binding site (CACCA) for the RUNX family of transcription factors, which could contribute to expression in both macrophages/osteoclasts (through AML1/runx1) and osteoblasts (through runx2)."[11]

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box), GACGTC (C box), TACGTA (A box), AACGTT (T box), and a GCN4 motif, namely TGA(G/C)TCA (Landschulz et al., 1988;[12] Nijhawan et al., 2008[13])."[14]

"The human [transforming growth factor b1] TGF-β1 promoter region contains two binding sequences for [activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."[15]

"The program DNA-Pattern was used to search for and catalogue occurrences of consensus GCRE (TGABTVW) [TGA(C/G/T)T(A/C/G)(A/T)] and GATA (GATAAG, GATAAH, GATTA) motifs in yeast promoters."[16]

"The predicted Gln3p and Gcn4p binding sites in the UGA3 promoter are [...] the consensus Gln3p (GATA) and Gcn4p (GCRE) [TGAGTCA] binding sites present in the minimal UGA3 promoter at -􏰉206 and -􏰉112, respectively, [...]."[16]

"Saccharomyces cerevisiae contains eight members of a novel and fungus-specific family of bZIP proteins that is defined by four atypical residues on the DNA-binding surface. Two of these proteins, Yap1 and Yap2, are transcriptional activators involved in pleiotropic drug resistance. Although initially described as AP-1 factors, at least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA); further, a Yap-like derivative of the AP-1 factor Gcn4 (A239Q S242F) binds efficiently to the Yap recognition sequence."[17]

Activating protein samplings (Cohen)

Copying GCCTGGCC[10] in "⌘F" yields none between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GCCTGGCC-3'[10] (starting with SuccessablesAPCo.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, negative direction, looking for 5'-GCCTGGCC-3', 0.
  2. negative strand, positive direction, looking for 5'-GCCTGGCC-3', 2, 5'-GCCTGGCC-3' at 3681, 5'-GCCTGGCC-3' at 2990.
  3. Positive strand, negative direction, looking for 5'-GCCTGGCC-3', 2, 5'-GCCTGGCC-3' at 3130, 5'-GCCTGGCC-3' at 1200.
  4. positive strand, positive direction, looking for 5'-GCCTGGCC-3', 0.
  5. complement inverse, negative strand, negative direction, looking for 5'-GGCCAGGC-3', 0.
  6. complement inverse, negative strand, positive direction, looking for 5'-GGCCAGGC-3', 1, 5'-GGCCAGGC-3' at 1176.
  7. complement inverse, positive strand, negative direction, looking for 5'-GGCCAGGC-3', 3, 5'-GGCCAGGC-3' at 4103, 5'-GGCCAGGC-3' at 2520, 5'-GGCCAGGC-3' at 649.
  8. complement inverse, positive strand, positive direction, looking for 5'-GGCCAGGC-3', 0.

APCo (4560-2846) UTRs

  1. Positive strand, negative direction: GGCCAGGC at 4103, GCCTGGCC at 3130.

APCo negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: GGCCAGGC at 2520, GCCTGGCC at 1200, GGCCAGGC at 649.

APCo positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GCCTGGCC at 3681, GCCTGGCC at 2990, GGCCAGGC at 1176.

Activating protein (Cohen1) random dataset samplings

  1. Cor0: 0.
  2. Cor1: 0.
  3. Cor2: 0.
  4. Cor3: 0.
  5. Cor4: 0.
  6. Cor5: 0.
  7. Cor6: 0.
  8. Cor7: 0.
  9. Cor8: 0.
  10. Cor9: 0.
  11. Cor0ci: 0.
  12. Cor1ci: 0.
  13. Cor2ci: 0.
  14. Cor3ci: 0.
  15. Cor4ci: 0.
  16. Cor5ci: 0.
  17. Cor6ci: 0.
  18. Cor7ci: 0.
  19. Cor8ci: 0.
  20. Cor9ci: 0.

Activating protein (Cohen1) analysis and results

Main article: Complex locus A1BG and ZNF497 § APCo1s

Consensus sequences for the Activating protein 2 (AP-2) are GCCTGGCC.[10]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 3 2 1.5 1.5
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 3 2 1.4 1.5
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real Activating protein (Cohen1)s are greater than the randoms. This suggests that the real Activating protein (Cohen1)s are likely active or activable.

Activating protein (Cohen2) samplings

For the Basic programs testing consensus sequence 5'-TCCCCCGCCC-3' (starting with SuccessablesAPCo2.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, negative direction, looking for 5'-TCCCCCGCCC-3', 0.
  2. negative strand, positive direction, looking for 5'-TCCCCCGCCC-3', 0.
  3. positive strand, negative direction, looking for 5'-TCCCCCGCCC-3', 0.
  4. positive strand, positive direction, looking for 5'-TCCCCCGCCC-3', 1, 5'-TCCCCCGCCC-3' at 4440.
  5. complement, negative strand, negative direction, looking for 5'-AGGGGGCGGG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AGGGGGCGGG-3', 1, 5'-AGGGGGCGGG-3' at 4440.
  7. complement, positive strand, negative direction, looking for 5'-AGGGGGCGGG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-AGGGGGCGGG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GGGCGGGGGA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GGGCGGGGGA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GGGCGGGGGA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GGGCGGGGGA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CCCGCCCCCT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CCCGCCCCCT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CCCGCCCCCT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CCCGCCCCCT-3', 0.

Activating protein (Cohen2) core promoters

Positive strand, positive direction: TCCCCCGCCC at 4440, with the TSS at 4300 nts.

Activating protein (Cohen) random dataset samplings

  1. APCo2r0: 0.
  2. APCo2r1: 0.
  3. APCo2r2: 0.
  4. APCo2r3: 0.
  5. APCo2r4: 0.
  6. APCo2r5: 0.
  7. APCo2r6: 0.
  8. APCo2r7: 0.
  9. APCo2r8: 0.
  10. APCo2r9: 0.
  11. APCo2r0ci: 0.
  12. APCo2r1ci: 0.
  13. APCo2r2ci: 0.
  14. APCo2r3ci: 0.
  15. APCo2r4ci: 0.
  16. APCo2r5ci: 0.
  17. APCo2r6ci: 0.
  18. APCo2r7ci: 0.
  19. APCo2r8ci: 0.
  20. APCo2r9ci: 0.

Activating protein (Cohen2) analysis and results

Main article: Complex locus A1BG and ZNF497 § APCo2s

Consensus sequence is TCCCCCGCCC.[10]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 1 2 0.5 0.5
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real activating protein (Cohen2)s are greater than the randoms. This suggests that the real activating protein (Cohen2)s are likely active or activable.

AP-2 samplings

Main article: Model samplings

Consensus sequences for the Activating protein 2 (AP-2) are TCTTCCC and CTCCCA.[18]

Activating protein samplings (Yao1)

Copying 5'-TCTTCCC-3' in "⌘F" yields one between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TCTTCCC-3'[18] (starting with SuccessablesAP.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, negative direction, looking for 5'-TCTTCCC-3', 1, TCTTCCC at 1657.
  2. negative strand, positive direction, looking for 5'-TCTTCCC-3', 0.
  3. positive strand, negative direction, looking for 5'-TCTTCCC-3', 0.
  4. positive strand, positive direction, looking for 5'-TCTTCCC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-AGAAGGG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AGAAGGG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-AGAAGGG-3', 1, 5'-AGAAGGG-3' at 1657.
  8. complement, positive strand, positive direction, looking for 5'-AGAAGGG-3', 0.
  9. complement inverse, negative strand, negative direction, looking for 5'-GGGAAGA-3', 1, GGGAAGA at 620.
  10. complement inverse, negative strand, positive direction, looking for GGGAAGA, 1, GGGAAGA at 4264.
  11. complement inverse, positive strand, negative direction, looking for 5'-GGGAAGA-3', 0.
  12. complement inverse, positive strand, positive direction, looking for 5'-GGGAAGA-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-CCCTTCT-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-CCCTTCT-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-CCCTTCT-3', 1, 5'-CCCTTCT-3' at 620.
  16. inverse, positive strand, positive direction, looking for 5'-CCCTTCT-3', 1, 5'-CCCTTCT-3' at 4264.

Activating protein proximal promoters (Yao1)

Negative strand, positive direction: GGGAAGA at 4264.

Activating protein distal promoters (Yao1)

Negative strand, negative direction: TCTTCCC at 1657, GGGAAGA at 620.

Yao1 random dataset samplings

  1. Yao1r0: 0.
  2. Yao1r1: 0.
  3. Yao1r2: 1, TCTTCCC at 924.
  4. Yao1r3: 0.
  5. Yao1r4: 0.
  6. Yao1r5: 0.
  7. Yao1r6: 0.
  8. Yao1r7: 1, TCTTCCC at 1201.
  9. Yao1r8: 1, TCTTCCC at 3951.
  10. Yao1r9: 1, TCTTCCC at 1995.
  11. Yao1r0ci: 0.
  12. Yao1r1ci: 1, GGGAAGA at 468.
  13. Yao1r2ci: 0.
  14. Yao1r3ci: 0.
  15. Yao1r4ci: 0.
  16. Yao1r5ci: 1, GGGAAGA at 1193.
  17. Yao1r6ci: 0.
  18. Yao1r7ci: 0.
  19. Yao1r8ci: 1, GGGAAGA at 4383.
  20. Yao1r9ci: 0.

Yao1r arbitrary (evens) (4560-2846) UTRs

  1. Yao1r8: TCTTCCC at 3951.
  2. Yao1r8ci: GGGAAGA at 4383.

Yao1r alternate positive direction (evens) (4445-4265) core promoters

  1. Yao1r8ci: GGGAAGA at 4383.

Yao1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Yao1r2: TCTTCCC at 924.

Yao1r alternate negative direction (odds) (2596-1) distal promoters

  1. Yao1r7: TCTTCCC at 1201.
  2. Yao1r9: TCTTCCC at 1995.
  3. Yao1r1ci: GGGAAGA at 468.
  4. Yao1r5ci: GGGAAGA at 1193.

Yao1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Yao1r7: TCTTCCC at 1201.
  2. Yao1r9: TCTTCCC at 1995.
  3. Yao1r1ci: GGGAAGA at 468.
  4. Yao1r5ci: GGGAAGA at 1193.

Yao1r alternate positive direction (evens) (4050-1) distal promoters

  1. Yao1r2: TCTTCCC at 924.
  2. Yao1r8: TCTTCCC at 3951.

Activating protein 2 (Yao1) analysis and results

Main article: Complex locus A1BG and ZNF497 § Yao1s

Consensus sequences for the Activating protein 2 (AP-2) is TCTTCCC.[18]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 2 10 0.2 0.1
Randoms UTR alternate negative 0 10 0 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 1 2 0.5 0.5
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 2 2 1 1
Randoms Distal arbitrary negative 1 10 0.1 0.25
Randoms Distal alternate negative 4 10 0.4 0.25
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 4 10 0.4 0.3
Randoms Distal alternate positive 2 10 0.2 0.3

Comparison:

The occurrences of real Activating protein 2 (Yao1)s are greater than the randoms. This suggests that the real Activating protein 2 (Yao1)s are likely active or activable.

Activating protein samplings (Yao2)

Copying 5'-CTCCCA-3' in "⌘F" yields none between ZSCAN22 and A1BG and five between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CTCCCA (based on the mouse and rat DRE consensus complement GAGGGT and complement inverse TGGGAG)[18][19] (starting with SuccessablesAP.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, negative direction: 0.
  2. negative strand, positive direction: CTCCCA at 3333, CTCCCA at 2532, CTCCCA at 2396, CTCCCA at 2383, CTCCCA at 466.
  3. positive strand, negative direction: CTCCCA at 4259, CTCCCA at 389.
  4. positive strand, positive direction: CTCCCA at 3880, CTCCCA at 2797, CTCCCA at 182.
  5. complement inverse, negative strand, negative direction: 0.
  6. complement inverse, negative strand, positive direction: TGGGAG at 1782.
  7. complement inverse, positive strand, negative direction: TGGGAG at 4549, TGGGAG at 4497, TGGGAG at 4303, TGGGAG at 4271, TGGGAG at 4153, TGGGAG at 3989, TGGGAG at 3752, TGGGAG at 3714, TGGGAG at 3080, TGGGAG at 2221, TGGGAG at 2104, TGGGAG at 1962, TGGGAG at 1930, TGGGAG at 1795, TGGGAG at 1018, TGGGAG at 686, TGGGAG at 550, TGGGAG at 413.
  8. complement inverse, positive strand, positive direction: 0.

APY2 (4560-2846) UTRs

  1. Positive strand, negative direction: TGGGAG at 4549, TGGGAG at 4497, TGGGAG at 4303, TGGGAG at 4271, CTCCCA at 4259, TGGGAG at 4153, TGGGAG at 3989, TGGGAG at 3752, TGGGAG at 3714, TGGGAG at 3080.

APY2 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TGGGAG at 2221, TGGGAG at 2104, TGGGAG at 1962, TGGGAG at 1930, TGGGAG at 1795, TGGGAG at 1018, TGGGAG at 686, TGGGAG at 550, TGGGAG at 413, CTCCCA at 389.

APY2 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CTCCCA at 3333, CTCCCA at 2532, CTCCCA at 2396, CTCCCA at 2383, TGGGAG at 1782, CTCCCA at 466.
  2. Positive strand, positive direction: CTCCCA at 3880, CTCCCA at 2797, CTCCCA at 182.

Yao2 random dataset samplings

  1. Yao2r0: 1, CTCCCA at 1519.
  2. Yao2r1: 1, CTCCCA at 1225.
  3. Yao2r2: 0.
  4. Yao2r3: 2, CTCCCA at 3832, CTCCCA at 1726.
  5. Yao2r4: 2, CTCCCA at 3641, CTCCCA at 2543.
  6. Yao2r5: 0.
  7. Yao2r6: 3, CTCCCA at 1295, CTCCCA at 850, CTCCCA at 690.
  8. Yao2r7: 0.
  9. Yao2r8: 2, CTCCCA at 3253, CTCCCA at 3037.
  10. Yao2r9: 4, CTCCCA at 3945, CTCCCA at 3405, CTCCCA at 2242, CTCCCA at 1781.
  11. Yao2r0ci: 1, TGGGAG at 938.
  12. Yao2r1ci: 0.
  13. Yao2r2ci: 2, TGGGAG at 286, TGGGAG at 190.
  14. Yao2r3ci: 1, TGGGAG at 1621.
  15. Yao2r4ci: 2, TGGGAG at 3112, TGGGAG at 2705.
  16. Yao2r5ci: 4, TGGGAG at 3153, TGGGAG at 2750, TGGGAG at 2583, TGGGAG at 920.
  17. Yao2r6ci: 1, TGGGAG at 3828.
  18. Yao2r7ci: 2, TGGGAG at 4155, TGGGAG at 2869.
  19. Yao2r8ci: 2, TGGGAG at 2644, TGGGAG at 1327.
  20. Yao2r9ci: 1, TGGGAG at 40.

APY2r arbitrary (evens) (4560-2846) UTRs

  1. Yao2r4: CTCCCA at 3641.
  2. Yao2r8: CTCCCA at 3253, CTCCCA at 3037.
  3. Yao2r4ci: TGGGAG at 3112.
  4. Yao2r6ci: TGGGAG at 3828.

APY2r alternate (odds) (4560-2846) UTRs

  1. Yao2r3: CTCCCA at 3832.
  2. Yao2r9: CTCCCA at 3945, CTCCCA at 3405.
  3. Yao2r5ci: TGGGAG at 3153.
  4. Yao2r7ci: TGGGAG at 4155, TGGGAG at 2869.

APY2r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Yao2r4ci: TGGGAG at 2705.
  2. Yao2r8ci: TGGGAG at 2644.

APY2r alternate negative direction (odds) (2811-2596) proximal promoters

  1. Yao2r5ci: TGGGAG at 2750.

APY2r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Yao2r7ci: TGGGAG at 4155.

APY2r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Yao2r0: CTCCCA at 1519.
  2. Yao2r4: CTCCCA at 2543.
  3. Yao2r6: CTCCCA at 1295, CTCCCA at 850, CTCCCA at 690.
  4. Yao2r0ci: TGGGAG at 938.
  5. Yao2r2ci: TGGGAG at 286, TGGGAG at 190.
  6. Yao2r8ci: TGGGAG at 1327.

APY2r alternate negative direction (odds) (2596-1) distal promoters

  1. Yao2r1: CTCCCA at 1225.
  2. Yao2r3: CTCCCA at 1726.
  3. Yao2r9: CTCCCA at 2242, CTCCCA at 1781.
  4. Yao2r3ci: TGGGAG at 1621.
  5. Yao2r5ci: TGGGAG at 2583, TGGGAG at 920.
  6. Yao2r9ci: TGGGAG at 40.

APY2r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Yao2r1: CTCCCA at 1225.
  2. Yao2r3: CTCCCA at 3832, CTCCCA at 1726.
  3. Yao2r9: CTCCCA at 3945, CTCCCA at 3405, CTCCCA at 2242, CTCCCA at 1781.
  4. Yao2r3ci: TGGGAG at 1621.
  5. Yao2r5ci: TGGGAG at 3153, TGGGAG at 2750, TGGGAG at 2583, TGGGAG at 920.
  6. Yao2r7ci: TGGGAG at 2869.
  7. Yao2r9ci: TGGGAG at 40.

APY2r alternate positive direction (evens) (4050-1) distal promoters

  1. Yao2r0: CTCCCA at 1519.
  2. Yao2r4: CTCCCA at 3641, CTCCCA at 2543.
  3. Yao2r6: CTCCCA at 1295, CTCCCA at 850, CTCCCA at 690.
  4. Yao2r8: CTCCCA at 3253, CTCCCA at 3037.
  5. Yao2r0ci: TGGGAG at 938.
  6. Yao2r2ci: TGGGAG at 286, TGGGAG at 190.
  7. Yao2r4ci: TGGGAG at 3112, TGGGAG at 2705.
  8. Yao2r6ci: TGGGAG at 3828.
  9. Yao2r8ci: TGGGAG at 2644, TGGGAG at 1327.

Activating protein 2 (Yao2) analysis and results

Main article: Complex locus A1BG and ZNF497 § Yao2s

Consensus sequences for the Activating protein 2 (AP-2) is CTCCCA.[18]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 10 2 5 5 ± 5 (--0,+-10)
Randoms UTR arbitrary negative 5 10 0.5 0.55
Randoms UTR alternate negative 6 10 0.6 0.55
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 2 10 0.2 0.15
Randoms Proximal alternate negative 1 10 0.1 0.15
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 10 2 5 5 ± 5 (--0,+-10)
Randoms Distal arbitrary negative 9 10 0.9 0.85
Randoms Distal alternate negative 8 10 0.8 0.85
Reals Distal positive 9 2 4.5 4.5 ± 1.5 (-+6,++3)
Randoms Distal arbitrary positive 14 10 1.4 1.5
Randoms Distal alternate positive 16 10 1.6 1.5

Comparison:

The occurrences of real AP2Yao2 UTRs and distals, positive strand, negative direction, and positive direction distals are greater than the randoms. This suggests that the real AP2Yao2s are likely active or activable.

Activating protein samplings (Yao3)

For the Basic programs testing consensus sequence GGCCAA (from TCDD*AhR DNA-binding consensus sequence of GCGTGNN(A/T)NNN(C/G))[18] (starting with SuccessablesYao3.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, negative direction, looking for GGCCAA, 0.
  2. negative strand, positive direction, looking for GGCCAA, 5, GGCCAA at 2609, GGCCAA at 1202, GGCCAA at 691, GGCCAA at 555, GGCCAA at 418.
  3. positive strand, negative direction, looking for GGCCAA, 0.
  4. positive strand, positive direction, looking for GGCCAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTGGCC, 0.
  6. inverse complement, negative strand, positive direction, looking for TTGGCC, 0.
  7. inverse complement, positive strand, negative direction, looking for TTGGCC, 3, TTGGCC at 4099, TTGGCC at 3948, TTGGCC at 645.
  8. inverse complement, positive strand, positive direction, looking for TTGGCC, 0.

APY3 (4560-2846) UTRs

  1. Positive strand, negative direction: TTGGCC at 4099, TTGGCC at 3948.

APY3 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TTGGCC at 645.

APY3 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GGCCAA at 2609, GGCCAA at 1202, GGCCAA at 691, GGCCAA at 555, GGCCAA at 418.

Yao3 random dataset samplings

  1. Yao3r0: 2, GGCCAA at 4456, GGCCAA at 3350.
  2. Yao3r1: 1, GGCCAA at 842.
  3. Yao3r2: 2, GGCCAA at 2263, GGCCAA at 1224.
  4. Yao3r3: 1, GGCCAA at 1593.
  5. Yao3r4: 3, GGCCAA at 3268, GGCCAA at 790, GGCCAA at 716.
  6. Yao3r5: 2, GGCCAA at 3077, GGCCAA at 1995.
  7. Yao3r6: 2, GGCCAA at 3203, GGCCAA at 739.
  8. Yao3r7: 1, GGCCAA at 2301.
  9. Yao3r8: 4, GGCCAA at 3897, GGCCAA at 3813, GGCCAA at 671, GGCCAA at 384.
  10. Yao3r9: 0.
  11. Yao3r0ci: 3, TTGGCC at 3853, TTGGCC at 2641, TTGGCC at 306.
  12. Yao3r1ci: 1, TTGGCC at 4086.
  13. Yao3r2ci: 1, TTGGCC at 4539.
  14. Yao3r3ci: 3, TTGGCC at 1518, TTGGCC at 1115, TTGGCC at 668.
  15. Yao3r4ci: 0.
  16. Yao3r5ci: 2, TTGGCC at 4423, TTGGCC at 356.
  17. Yao3r6ci: 0.
  18. Yao3r7ci: 3, TTGGCC at 4384, TTGGCC at 3299, TTGGCC at 1236.
  19. Yao3r8ci: 1, TTGGCC at 1005.
  20. Yao3r9ci: 1, TTGGCC at 1840.

APY3r arbitrary (evens) (4560-2846) UTRs

  1. Yao3r0: GGCCAA at 4456, GGCCAA at 3350.
  2. Yao3r4: GGCCAA at 3268.
  3. Yao3r6: GGCCAA at 3203.
  4. Yao3r8: GGCCAA at 3897, GGCCAA at 3813.
  5. Yao3r0ci: TTGGCC at 3853.
  6. Yao3r2ci: TTGGCC at 4539.

APY3r alternate (odds) (4560-2846) UTRs

  1. Yao3r5: GGCCAA at 3077.
  2. Yao3r1ci: TTGGCC at 4086.
  3. Yao3r5ci: TTGGCC at 4423.
  4. Yao3r7ci: TTGGCC at 4384, TTGGCC at 3299.

APY3r arbitrary positive direction (odds) (4445-4265) core promoters

  1. Yao3r5ci: TTGGCC at 4423.
  2. Yao3r7ci: TTGGCC at 4384.

APY3r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Yao3r0ci: TTGGCC at 2641.

APY3r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Yao3r1ci: TTGGCC at 4086.

APY3r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Yao3r2: GGCCAA at 2263, GGCCAA at 1224.
  2. Yao3r4: GGCCAA at 790, GGCCAA at 716.
  3. Yao3r6: GGCCAA at 739.
  4. Yao3r8: GGCCAA at 671, GGCCAA at 384.
  5. Yao3r0ci: TTGGCC at 306.
  6. Yao3r8ci: TTGGCC at 1005.

APY3r alternate negative direction (odds) (2596-1) distal promoters

  1. Yao3r1: GGCCAA at 842.
  2. Yao3r3: GGCCAA at 1593.
  3. Yao3r5: GGCCAA at 1995.
  4. Yao3r7: GGCCAA at 2301.
  5. Yao3r3ci: TTGGCC at 1518, TTGGCC at 1115, TTGGCC at 668.
  6. Yao3r5ci: TTGGCC at 356.
  7. Yao3r7ci: TTGGCC at 1236.
  8. Yao3r9ci: TTGGCC at 1840.

APY3r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Yao3r1: GGCCAA at 842.
  2. Yao3r3: GGCCAA at 1593.
  3. Yao3r5: GGCCAA at 3077, GGCCAA at 1995.
  4. Yao3r7: GGCCAA at 2301.
  5. Yao3r3ci: TTGGCC at 1518, TTGGCC at 1115, TTGGCC at 668.
  6. Yao3r5ci: TTGGCC at 356.
  7. Yao3r7ci: TTGGCC at 3299, TTGGCC at 1236.
  8. Yao3r9ci: TTGGCC at 1840.

APY3r alternate positive direction (evens) (4050-1) distal promoters

  1. Yao3r0: GGCCAA at 3350.
  2. Yao3r2: GGCCAA at 2263, GGCCAA at 1224.
  3. Yao3r4: GGCCAA at 3268, GGCCAA at 790, GGCCAA at 716.
  4. Yao3r6: GGCCAA at 3203, GGCCAA at 739.
  5. Yao3r8: GGCCAA at 3897, GGCCAA at 3813, GGCCAA at 671, GGCCAA at 384.
  6. Yao3r0ci: TTGGCC at 3853, TTGGCC at 2641, TTGGCC at 306.
  7. Yao3r8ci: TTGGCC at 1005.

Activating protein 2 (Yao3) analysis and results

Main article: Complex locus A1BG and ZNF497 § Yau3s

Consensus sequence GGCCAA (from TCDD*AhR DNA-binding consensus sequence of GCGTGNN(A/T)NNN(C/G)).[18]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 8 10 0.8 0.65
Randoms UTR alternate negative 5 10 0.5 0.65
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 2 10 0.2 0.1
Randoms Core alternate positive 0 10 0 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 1 2 0.5 0.5
Randoms Distal arbitrary negative 9 10 0.9 0.95
Randoms Distal alternate negative 10 10 1 0.95
Reals Distal positive 5 2 2.5 2.5
Randoms Distal arbitrary positive 12 10 1.2 1.4
Randoms Distal alternate positive 16 10 1.6 1.4

Comparison:

The occurrences of real activating protein 2 (Yao3) UTRs are greater than the randoms, the negative direction distals are less than the randoms and the positive direction distals are greater than the randoms. This suggests that the real activating protein 2 (Yao3)s are likely active or activable.

Activating protein samplings (Murata, 3N)

For the Basic programs testing consensus sequence 5'-(C/G)CCNNNGG(C/G)-3'[9] (starting with SuccessablesAP.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, negative direction: 1, CCCTGCGGC at 1154.
  2. Negative strand, positive direction: 12, CCCTGGGGC at 4427, CCCTTGGGG at 4302, CCCATGGGG at 4224, CCCCATGGG at 4223, GCCCTGGGC at 3498, GCCAATGGG at 2911, GCCTCTGGC at 2884, CCCTTAGGG at 2766, GCCACCGGC at 1547, GCCACCGGC at 1295, GCCAGCGGC at 332, CCCTCAGGC at 91.
  3. Positive strand, negative direction: 1, CCCAAGGGC at 1820.
  4. positive strand, positive direction: 10, CCCGTTGGC at 3912, CCCTGTGGG at 3533, GCCAACGGG at 3493, CCCAGAGGC at 1961, GCCGGTGGG at 1852, GCCCGCGGG at 1770, CCCGGCGGC at 1758, GCCCCCGGC at 1647, CCCGACGGC at 483, CCCTCCGGG at 372.

Complement inverse is the same as the direct.

APM positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CCCTGGGGC at 4427, CCCTTGGGG at 4302.

APM positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: CCCATGGGG at 4224, CCCCATGGG at 4223.

APM negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCCTGCGGC at 1154.
  2. Positive strand, negative direction: CCCAAGGGC at 1820.

APM positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GCCCTGGGC at 3498, GCCAATGGG at 2911, GCCTCTGGC at 2884, CCCTTAGGG at 2766, GCCACCGGC at 1547, GCCACCGGC at 1295, GCCAGCGGC at 332, CCCTCAGGC at 91.
  2. Positive strand, positive direction: CCCGTTGGC at 3912, CCCTGTGGG at 3533, GCCAACGGG at 3493, CCCAGAGGC at 1961, GCCGGTGGG at 1852, GCCCGCGGG at 1770, CCCGGCGGC at 1758, GCCCCCGGC at 1647, CCCGACGGC at 483, CCCTCCGGG at 372.

Activating protein (Murata, 3N) random dataset samplings

  1. APMr0: 6, CCCGCCGGG at 4333, GCCGGTGGC at 4263, GCCGCAGGC at 3245, GCCTGGGGG at 2319, GCCGAAGGG at 451, GCCAGGGGG at 68.
  2. APMr1: 8, CCCTTAGGG at 4537, GCCGAGGGG at 3134, CCCGAAGGG at 2384, GCCTTGGGG at 2008, GCCAAGGGG at 846, GCCCCCGGC at 720, GCCAGGGGC at 670, CCCCCCGGC at 122.
  3. APMr2: 11, GCCATAGGG at 4545, CCCTTTGGG at 4438, GCCAAGGGG at 3902, CCCCGGGGC at 3295, CCCAAAGGC at 3263, GCCAGGGGC at 2282, CCCTAGGGG at 1426, CCCACCGGG at 1132, CCCGGTGGC at 817, CCCTGTGGC at 460, CCCGTCGGG at 91.
  4. APMr3: 11, GCCGACGGG at 4509, CCCTTAGGG at 4124, CCCACCGGC at 3837, GCCCGGGGG at 3752, CCCTGCGGC at 3413, GCCCGGGGC at 3403, CCCTTAGGG at 2648, CCCGACGGG at 2431, GCCGCCGGC at 1455, CCCAAAGGG at 1226, CCCTGAGGC at 380.
  5. APMr4: 16, CCCTAGGGC at 4177, CCCAAGGGG at 3568, CCCCAAGGG at 3567, GCCTTGGGC at 3547, GCCCCTGGC at 3232, CCCACGGGC at 3161, CCCCACGGG at 3160, CCCCCTGGG at 3110, GCCACTGGG at 2687, GCCTAGGGG at 1990, CCCGGGGGC at 1468, GCCCTGGGG at 1170, GCCGCCGGC at 1025, CCCGGAGGG at 1017, CCCCGGGGC at 351, GCCCTGGGG at 86.
  6. APMr5: 7, GCCCAGGGC at 4370, GCCGTCGGG at 2881, CCCGGGGGC at 2032, CCCCGGGGG at 2031, CCCATCGGG at 812, GCCAGCGGC at 685, GCCCTTGGC at 355.
  7. APMr6: 12, CCCTATGGG at 4345, GCCGGCGGG at 4289, GCCCCAGGG at 3515, CCCATTGGG at 3234, CCCCAAGGG at 2961, CCCAATGGC at 1958, CCCAAAGGG at 1681, CCCACCGGG at 1408, GCCCCAGGC at 685, GCCATCGGG at 463, GCCGTGGGG at 338, GCCGAGGGG at 110.
  8. APMr7: 7, GCCGGGGGG at 3946, CCCAGTGGG at 2867, CCCGCGGGG at 2749, GCCCGCGGG at 2748, CCCGGGGGC at 1377, CCCCTGGGC at 784, GCCCCTGGG at 783.
  9. APMr8: 13, CCCGGGGGG at 3460, GCCCGGGGG at 3459, GCCGGGGGC at 3319, CCCTTGGGG at 2455, CCCCTTGGG at 2454, CCCCGAGGC at 2282, GCCCGAGGG at 2018, CCCTTCGGG at 1613, GCCCACGGC at 944, GCCGGAGGG at 686, CCCGTGGGC at 186, CCCCGTGGG at 185, GCCAACGGC at 131.
  10. APMr9: 9, CCCGATGGG at 4529, CCCCGTGGG at 3275, CCCTTGGGG at 3052, GCCCGTGGC at 2944, CCCAAGGGG at 2438, GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

APMr arbitrary (evens) (4560-2846) UTRs

  1. APMr0: CCCGCCGGG at 4333, GCCGGTGGC at 4263, GCCGCAGGC at 3245.
  2. APMr2: GCCATAGGG at 4545, CCCTTTGGG at 4438, GCCAAGGGG at 3902, CCCCGGGGC at 3295, CCCAAAGGC at 3263.
  3. APMr4: CCCTAGGGC at 4177, CCCAAGGGG at 3568, CCCCAAGGG at 3567, GCCTTGGGC at 3547, GCCCCTGGC at 3232, CCCACGGGC at 3161, CCCCACGGG at 3160, CCCCCTGGG at 3110.
  4. APMr6: CCCTATGGG at 4345, GCCGGCGGG at 4289, GCCCCAGGG at 3515, CCCATTGGG at 3234, CCCCAAGGG at 2961.
  5. APMr8: CCCGGGGGG at 3460, GCCCGGGGG at 3459, GCCGGGGGC at 3319.

APMr alternate (odds) (4560-2846) UTRs

  1. APMr1: CCCTTAGGG at 4537, GCCGAGGGG at 3134.
  2. APMr3: GCCGACGGG at 4509, CCCTTAGGG at 4124, CCCACCGGC at 3837, GCCCGGGGG at 3752, CCCTGCGGC at 3413, GCCCGGGGC at 3403.
  3. APMr5: GCCCAGGGC at 4370, GCCGTCGGG at 2881.
  4. APMr7: GCCGGGGGG at 3946, CCCAGTGGG at 2867.
  5. APMr9: CCCGATGGG at 4529, CCCCGTGGG at 3275, CCCTTGGGG at 3052, GCCCGTGGC at 2944.

APMr arbitrary positive direction (odds) (4445-4265) core promoters

  1. APMr5: GCCCAGGGC at 4370.

APMr alternate positive direction (evens) (4445-4265) core promoters

  1. APMr0: CCCGCCGGG at 4333.
  2. APMr2: CCCTTTGGG at 4438.
  3. APMr6: CCCTATGGG at 4345, GCCGGCGGG at 4289.

APMr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. APMr4: GCCACTGGG at 2687.

APMr alternate negative direction (odds) (2811-2596) proximal promoters

  1. APMr3: CCCTTAGGG at 2648.
  2. APMr7: CCCGCGGGG at 2749, GCCCGCGGG at 2748.

APMr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. APMr3: CCCTTAGGG at 4124.

APMr alternate positive direction (evens) (4265-4050) proximal promoters

  1. APMr0: GCCGGTGGC at 4263.
  2. APMr4: CCCTAGGGC at 4177.

APMr arbitrary negative direction (evens) (2596-1) distal promoters

  1. APMr0: GCCTGGGGG at 2319, GCCGAAGGG at 451, GCCAGGGGG at 68.
  2. APMr2: GCCAGGGGC at 2282, CCCTAGGGG at 1426, CCCACCGGG at 1132, CCCGGTGGC at 817, CCCTGTGGC at 460, CCCGTCGGG at 91.
  3. APMr4: GCCTAGGGG at 1990, CCCGGGGGC at 1468, GCCCTGGGG at 1170, GCCGCCGGC at 1025, CCCGGAGGG at 1017, CCCCGGGGC at 351, GCCCTGGGG at 86.
  4. APMr6: CCCAATGGC at 1958, CCCAAAGGG at 1681, CCCACCGGG at 1408, GCCCCAGGC at 685, GCCATCGGG at 463, GCCGTGGGG at 338, GCCGAGGGG at 110.
  5. APMr8: CCCTTGGGG at 2455, CCCCTTGGG at 2454, CCCCGAGGC at 2282, GCCCGAGGG at 2018, CCCTTCGGG at 1613, GCCCACGGC at 944, GCCGGAGGG at 686, CCCGTGGGC at 186, CCCCGTGGG at 185, GCCAACGGC at 131.

APMr alternate negative direction (odds) (2596-1) distal promoters

  1. APMr1: CCCGAAGGG at 2384, GCCTTGGGG at 2008, GCCAAGGGG at 846, GCCCCCGGC at 720, GCCAGGGGC at 670, CCCCCCGGC at 122.
  2. APMr3: CCCGACGGG at 2431, GCCGCCGGC at 1455, CCCAAAGGG at 1226, CCCTGAGGC at 380.
  3. APMr5: CCCGGGGGC at 2032, CCCCGGGGG at 2031, CCCATCGGG at 812, GCCAGCGGC at 685, GCCCTTGGC at 355.
  4. APMr7: CCCGGGGGC at 1377, CCCCTGGGC at 784, GCCCCTGGG at 783.
  5. APMr9: CCCAAGGGG at 2438, GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

APMr arbitrary positive direction (odds) (4050-1) distal promoters

  1. APMr1: GCCGAGGGG at 3134, CCCGAAGGG at 2384, GCCTTGGGG at 2008, GCCAAGGGG at 846, GCCCCCGGC at 720, GCCAGGGGC at 670, CCCCCCGGC at 122.
  2. APMr3: CCCACCGGC at 3837, GCCCGGGGG at 3752, CCCTGCGGC at 3413, GCCCGGGGC at 3403, CCCTTAGGG at 2648, CCCGACGGG at 2431, GCCGCCGGC at 1455, CCCAAAGGG at 1226, CCCTGAGGC at 380.
  3. APMr5: GCCGTCGGG at 2881, CCCGGGGGC at 2032, CCCCGGGGG at 2031, CCCATCGGG at 812, GCCAGCGGC at 685, GCCCTTGGC at 355.
  4. APMr7: GCCGGGGGG at 3946, CCCAGTGGG at 2867, CCCGCGGGG at 2749, GCCCGCGGG at 2748, CCCGGGGGC at 1377, CCCCTGGGC at 784, GCCCCTGGG at 783.
  5. APMr9: CCCCGTGGG at 3275, CCCTTGGGG at 3052, GCCCGTGGC at 2944, CCCAAGGGG at 2438, GCCCTCGGC at 2160, GCCTCCGGC at 1040, GCCGACGGC at 979, GCCCAAGGC at 340.

APMr alternate positive direction (evens) (4050-1) distal promoters

  1. APMr0: GCCGCAGGC at 3245, GCCTGGGGG at 2319, GCCGAAGGG at 451, GCCAGGGGG at 68.
  2. APMr2: GCCAAGGGG at 3902, CCCCGGGGC at 3295, CCCAAAGGC at 3263, GCCAGGGGC at 2282, CCCTAGGGG at 1426, CCCACCGGG at 1132, CCCGGTGGC at 817, CCCTGTGGC at 460, CCCGTCGGG at 91.
  3. APMr4: CCCAAGGGG at 3568, CCCCAAGGG at 3567, GCCTTGGGC at 3547, GCCCCTGGC at 3232, CCCACGGGC at 3161, CCCCACGGG at 3160, CCCCCTGGG at 3110, GCCACTGGG at 2687, GCCTAGGGG at 1990, CCCGGGGGC at 1468, GCCCTGGGG at 1170, GCCGCCGGC at 1025, CCCGGAGGG at 1017, CCCCGGGGC at 351, GCCCTGGGG at 86.
  4. APMr6: GCCCCAGGG at 3515, CCCATTGGG at 3234, CCCCAAGGG at 2961, CCCAATGGC at 1958, CCCAAAGGG at 1681, CCCACCGGG at 1408, GCCCCAGGC at 685, GCCATCGGG at 463, GCCGTGGGG at 338, GCCGAGGGG at 110.
  5. APMr8: CCCGGGGGG at 3460, GCCCGGGGG at 3459, GCCGGGGGC at 3319, CCCTTGGGG at 2455, CCCCTTGGG at 2454, CCCCGAGGC at 2282, GCCCGAGGG at 2018, CCCTTCGGG at 1613, GCCCACGGC at 944, GCCGGAGGG at 686, CCCGTGGGC at 186, CCCCGTGGG at 185, GCCAACGGC at 131.

Activating protein (Murata, 3N) analysis and results

Main article: Complex locus A1BG and ZNF497 § APM3Ns

"AP-2 proteins can bind to G/C-rich elements, such as 5’-[G/C]CCN(3,4)GG[G/C]-3’ (41, 42)."[9] Specifically, this is (C/G)CCNNNGG(C/G).[9]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 24 10 2.4 2.0
Randoms UTR alternate negative 16 10 1.6 2.0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 2 2 1 1
Randoms Core arbitrary positive 1 10 0.1 0.25
Randoms Core alternate positive 4 10 0.4 0.25
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.2
Randoms Proximal alternate negative 3 10 0.3 0.2
Reals Proximal positive 2 2 1 1
Randoms Proximal arbitrary positive 1 10 0.1 0.15
Randoms Proximal alternate positive 2 10 0.2 0.15
Reals Distal negative 2 2 1 1
Randoms Distal arbitrary negative 33 10 3.3 2.8
Randoms Distal alternate negative 23 10 2.3 2.8
Reals Distal positive 18 2 9 9 ± 1 (-+8,++10)
Randoms Distal arbitrary positive 37 10 3.7 4.4
Randoms Distal alternate positive 51 10 5.1 4.4

Comparison:

The occurrences of real APM positive direction cores, proximals and distals are greater than the randoms, negative direction distals are less than the randoms. This suggests that the real activating protein (Murata, 3N)s are likely active or activable.

Activating protein samplings (Murata, 4N)

For the Basic programs testing consensus sequence (C/G)CCNNNNGG(C/G)[9] (starting with SuccessablesAPM.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, negative direction: 0.
  2. Positive strand, negative direction: 2, GCCTTGAGGC at 3574, CCCAGGAGGC at 854.
  3. Negative strand, positive direction: 16, GCCTCCTGGG at 4410, CCCTTGGGGC at 4303, GCCTTCCGGG at 4245, CCCATGGGGG at 4225, CCCCATGGGG at 4224, GCCTCCAGGC at 3688, CCCAACAGGC at 3637, CCCGGGTGGG at 3562, GCCAATGGGC at 2912, CCCTTAGGGC at 2767, GCCTGCCGGG at 911, GCCTGCCGGG at 811, CCCGGCAGGG at 380, GCCACGAGGG at 245, CCCAAGAGGG at 181, CCCCTCAGGC at 91.
  4. Positive strand, positive direction: 6, CCCCAGAGGC at 1961, GCCCGGCGGC at 1758, GCCTCGTGGC at 1209, GCCCGACGGC at 483, CCCTCCGGGG at 373, CCCACCTGGG at 188.

Complement inverse is the same as the direct.

AP4N (4560-2846) UTRs

  1. Positive strand, negative direction: GCCTTGAGGC at 3574.

AP4N positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: GCCTCCTGGG at 4410, CCCTTGGGGC at 4303.

AP4N positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: GCCTTCCGGG at 4245, CCCATGGGGG at 4225, CCCCATGGGG at 4224.

AP4N negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: CCCAGGAGGC at 854.

AP4N positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GCCTCCAGGC at 3688, CCCAACAGGC at 3637, CCCGGGTGGG at 3562, GCCAATGGGC at 2912, CCCTTAGGGC at 2767, GCCTGCCGGG at 911, GCCTGCCGGG at 811, CCCGGCAGGG at 380, GCCACGAGGG at 245, CCCAAGAGGG at 181, CCCCTCAGGC at 91.
  2. Positive strand, positive direction: CCCCAGAGGC at 1961, GCCCGGCGGC at 1758, GCCTCGTGGC at 1209, GCCCGACGGC at 483, CCCTCCGGGG at 373, CCCACCTGGG at 188.

Activating protein (Murata, 4N) random dataset samplings

  1. AP4Nr0: 4, CCCGCCGGGC at 4334, CCCCGCCGGG at 4333, CCCTGAAGGC at 1631, GCCGAAGGGG at 452.
  2. AP4Nr1: 8, CCCTTAGGGG at 4538, GCCGAGGGGC at 3135, CCCGAAGGGC at 2385, CCCTTGTGGG at 873, GCCAAGGGGG at 847, GCCTGGAGGC at 728, GCCGGTCGGC at 512, CCCCCCCGGC at 122.
  3. AP4Nr2: 10, GCCATAGGGC at 4546, CCCTTTGGGG at 4439, GCCCTTTGGG at 4438, CCCTCTCGGC at 3648, GCCTATTGGC at 3593, GCCCAAAGGC at 3263, GCCTATAGGG at 3109, GCCAATAGGG at 2979, CCCAAGTGGG at 2606, GCCCGTCGGG at 91.
  4. AP4Nr3: 7, GCCGCCCGGG at 4142, CCCTGATGGC at 2875, CCCCGACGGG at 2431, CCCGTGAGGG at 2319, CCCATTAGGG at 1069, GCCGGCCGGC at 868, CCCCTGAGGC at 380.
  5. AP4Nr4: 11, CCCAAGGGGG at 3569, CCCCAAGGGG at 3568, CCCCCAAGGG at 3567, CCCCACGGGC at 3161, CCCCCACGGG at 3160, GCCCCCTGGG at 3110, CCCTCCTGGG at 2624, GCCTAGGGGC at 1991, GCCAAATGGC at 1365, CCCGGAGGGC at 1018, GCCCGGAGGG at 1017.
  6. AP4Nr5: 6, CCCACCAGGG at 3503, CCCGAACGGG at 3071, GCCGTGCGGG at 2972, GCCTAGTGGG at 2425, CCCCGGGGGC at 2032, GCCCATCGGG at 812.
  7. AP4Nr6: 13, CCCTATGGGG at 4346, CCCCTATGGG at 4345, GCCACCAGGC at 3912, CCCGGGTGGG at 3740, CCCATTGGGC at 3235, GCCCATTGGG at 3234, GCCCAATGGC at 1958, CCCAAAGGGG at 1682, GCCCAAAGGG at 1681, CCCACCGGGC at 1409, GCCCACCGGG at 1408, GCCATCGGGG at 464, GCCGAGGGGC at 111.
  8. AP4Nr7: 8, GCCTTATGGG at 3990, GCCGGGGGGG at 3947, GCCCGCGGGG at 2749, GCCGCTCGGG at 1915, GCCGCCTGGG at 1774, GCCACGAGGG at 1243, GCCCCTGGGC at 784, GCCGATAGGG at 154.
  9. AP4Nr8: 12, CCCGGGCGGG at 4122, CCCGGCCGGG at 3866, CCCGGGGGGG at 3461, GCCCGGGGGG at 3460, CCCTTGGGGG at 2456, CCCCTTGGGG at 2455, CCCCCTTGGG at 2454, GCCCCGAGGC at 2282, CCCTAGTGGG at 1566, CCCAGACGGC at 1386, CCCTAGTGGC at 754, CCCCGTGGGC at 186.
  10. AP4Nr9: 6, CCCCGATGGG at 4529, CCCATTTGGG at 3479, CCCCCGTGGG at 3275, CCCATCAGGG at 2676, CCCGAGAGGC at 2305, CCCAGGCGGG at 2135.

AP4Nr arbitrary (evens) (4560-2846) UTRs

  1. AP4Nr0: CCCGCCGGGC at 4334, CCCCGCCGGG at 4333.
  2. AP4Nr2: GCCATAGGGC at 4546, CCCTTTGGGG at 4439, GCCCTTTGGG at 4438, CCCTCTCGGC at 3648, GCCTATTGGC at 3593, GCCCAAAGGC at 3263, GCCTATAGGG at 3109, GCCAATAGGG at 2979.
  3. AP4Nr4: CCCAAGGGGG at 3569, CCCCAAGGGG at 3568, CCCCCAAGGG at 3567, CCCCACGGGC at 3161, CCCCCACGGG at 3160, GCCCCCTGGG at 3110.
  4. AP4Nr6: CCCTATGGGG at 4346, CCCCTATGGG at 4345, GCCACCAGGC at 3912, CCCGGGTGGG at 3740, CCCATTGGGC at 3235, GCCCATTGGG at 3234.
  5. AP4Nr8: CCCGGGCGGG at 4122, CCCGGCCGGG at 3866, CCCGGGGGGG at 3461, GCCCGGGGGG at 3460.

AP4Nr alternate (odds) (4560-2846) UTRs

  1. AP4Nr1: CCCTTAGGGG at 4538, GCCGAGGGGC at 3135.
  2. AP4Nr3: GCCGCCCGGG at 4142, CCCTGATGGC at 2875.
  3. AP4Nr5: CCCACCAGGG at 3503, CCCGAACGGG at 3071, GCCGTGCGGG at 2972.
  4. AP4Nr7: GCCTTATGGG at 3990, GCCGGGGGGG at 3947.
  5. AP4Nr9: CCCCGATGGG at 4529, CCCATTTGGG at 3479, CCCCCGTGGG at 3275.

AP4Nr alternate positive direction (evens) (4445-4265) core promoters

  1. AP4Nr0: CCCGCCGGGC at 4334, CCCCGCCGGG at 4333.
  2. AP4Nr2: CCCTTTGGGG at 4439, GCCCTTTGGG at 4438.
  3. AP4Nr6: CCCTATGGGG at 4346, CCCCTATGGG at 4345.

AP4Nr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. AP4Nr2: CCCAAGTGGG at 2606.
  2. AP4Nr4: CCCTCCTGGG at 2624.

AP4Nr alternate negative direction (odds) (2811-2596) proximal promoters

  1. AP4Nr7: GCCCGCGGGG at 2749.
  2. AP4Nr9: CCCATCAGGG at 2676.

AP4Nr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. AP4Nr3: GCCGCCCGGG at 4142.

AP4Nr alternate positive direction (evens) (4265-4050) proximal promoters

  1. AP4Nr8: CCCGGGCGGG at 4122.

AP4Nr arbitrary negative direction (evens) (2596-1) distal promoters

  1. AP4Nr0: CCCTGAAGGC at 1631, GCCGAAGGGG at 452.
  2. AP4Nr2: CCCAAGTGGG at 2606, GCCCGTCGGG at 91.
  3. AP4Nr4: GCCTAGGGGC at 1991, GCCAAATGGC at 1365, CCCGGAGGGC at 1018, GCCCGGAGGG at 1017.
  4. AP4Nr6: GCCCAATGGC at 1958, CCCAAAGGGG at 1682, GCCCAAAGGG at 1681, CCCACCGGGC at 1409, GCCCACCGGG at 1408, GCCATCGGGG at 464, GCCGAGGGGC at 111.
  5. AP4Nr8: CCCTTGGGGG at 2456, CCCCTTGGGG at 2455, CCCCCTTGGG at 2454, GCCCCGAGGC at 2282, CCCTAGTGGG at 1566, CCCAGACGGC at 1386, CCCTAGTGGC at 754, CCCCGTGGGC at 186.

AP4Nr alternate negative direction (odds) (2596-1) distal promoters

  1. AP4Nr1: CCCGAAGGGC at 2385, CCCTTGTGGG at 873, GCCAAGGGGG at 847, GCCTGGAGGC at 728, GCCGGTCGGC at 512, CCCCCCCGGC at 122.
  2. AP4Nr3: CCCCGACGGG at 2431, CCCGTGAGGG at 2319, CCCATTAGGG at 1069, GCCGGCCGGC at 868, CCCCTGAGGC at 380.
  3. AP4Nr5: GCCTAGTGGG at 2425, CCCCGGGGGC at 2032, GCCCATCGGG at 812.
  4. AP4Nr7: GCCGCTCGGG at 1915, GCCGCCTGGG at 1774, GCCACGAGGG at 1243, GCCCCTGGGC at 784, GCCGATAGGG at 154.
  5. AP4Nr9: CCCGAGAGGC at 2305, CCCAGGCGGG at 2135.

AP4Nr arbitrary positive direction (odds) (4050-1) distal promoters

  1. AP4Nr1: GCCGAGGGGC at 3135, CCCGAAGGGC at 2385, CCCTTGTGGG at 873, GCCAAGGGGG at 847, GCCTGGAGGC at 728, GCCGGTCGGC at 512, CCCCCCCGGC at 122.
  2. AP4Nr3: CCCTGATGGC at 2875, CCCCGACGGG at 2431, CCCGTGAGGG at 2319, CCCATTAGGG at 1069, GCCGGCCGGC at 868, CCCCTGAGGC at 380.
  3. AP4Nr5: CCCACCAGGG at 3503, CCCGAACGGG at 3071, GCCGTGCGGG at 2972, GCCTAGTGGG at 2425, CCCCGGGGGC at 2032, GCCCATCGGG at 812.
  4. AP4Nr7: GCCTTATGGG at 3990, GCCGGGGGGG at 3947, GCCCGCGGGG at 2749, GCCGCTCGGG at 1915, GCCGCCTGGG at 1774, GCCACGAGGG at 1243, GCCCCTGGGC at 784, GCCGATAGGG at 154.
  5. AP4Nr9: CCCATTTGGG at 3479, CCCCCGTGGG at 3275, CCCATCAGGG at 2676, CCCGAGAGGC at 2305, CCCAGGCGGG at 2135.

AP4Nr alternate positive direction (evens) (4050-1) distal promoters

  1. AP4Nr0: CCCTGAAGGC at 1631, GCCGAAGGGG at 452.
  2. AP4Nr2: CCCTCTCGGC at 3648, GCCTATTGGC at 3593, GCCCAAAGGC at 3263, GCCTATAGGG at 3109, GCCAATAGGG at 2979, CCCAAGTGGG at 2606, GCCCGTCGGG at 91.
  3. AP4Nr4: CCCAAGGGGG at 3569, CCCCAAGGGG at 3568, CCCCCAAGGG at 3567, CCCCACGGGC at 3161, CCCCCACGGG at 3160, GCCCCCTGGG at 3110, CCCTCCTGGG at 2624, GCCTAGGGGC at 1991, GCCAAATGGC at 1365, CCCGGAGGGC at 1018, GCCCGGAGGG at 1017.
  4. AP4Nr6: GCCACCAGGC at 3912, CCCGGGTGGG at 3740, CCCATTGGGC at 3235, GCCCATTGGG at 3234, GCCCAATGGC at 1958, CCCAAAGGGG at 1682, GCCCAAAGGG at 1681, CCCACCGGGC at 1409, GCCCACCGGG at 1408, GCCATCGGGG at 464, GCCGAGGGGC at 111.
  5. AP4Nr8: CCCGGCCGGG at 3866, CCCGGGGGGG at 3461, GCCCGGGGGG at 3460, CCCTTGGGGG at 2456, CCCCTTGGGG at 2455, CCCCCTTGGG at 2454, GCCCCGAGGC at 2282, CCCTAGTGGG at 1566, CCCAGACGGC at 1386, CCCTAGTGGC at 754, CCCCGTGGGC at 186.

Activating protein (Murata, 4N) analysis and results

Main article: Complex locus A1BG and ZNF497 § APM4Ns

"AP-2 proteins can bind to G/C-rich elements, such as 5’-[G/C]CCN(3,4)GG[G/C]-3’ (41, 42)."[9] Specifically, (C/G)CCNNNNGG(C/G).[9]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 26 10 2.6 1.9
Randoms UTR alternate negative 12 10 1.2 1.9
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 2 2 1 1
Randoms Core arbitrary positive 0 10 0 0.3
Randoms Core alternate positive 6 10 0.6 0.3
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 2 10 0.2 0.2
Randoms Proximal alternate negative 2 10 0.2 0.2
Reals Proximal positive 3 2 1.5 1.5
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 1 2 0.5 0.5
Randoms Distal arbitrary negative 23 10 2.3 2.2
Randoms Distal alternate negative 21 10 2.1 2.2
Reals Distal positive 17 2 8.5 8.5 ± 2.5(-+11,++6)
Randoms Distal arbitrary positive 32 10 3.2 3.7
Randoms Distal alternate positive 42 10 4.2 3.7

Comparison:

The occurrences of real activating protein (Murata, 4N) UTRs and negative direction distals are less than the randoms, positive direction cores, proximals, and distals are greater than the randoms. This suggests that the real activating protein (Murata, 4N)s are likely active or activable.

Target of Rapamycin (TOR) Regulatory Pathways

The mTOR pathway is a central regulator of mammalian metabolism and physiology, with important roles in the function of tissues including liver, muscle, white and brown adipose tissue,[20] and the brain, and is dysregulated in human diseases, such as diabetes, obesity, depression, and certain cancers.[21][22] Rapamycin inhibits mTOR by associating with its intracellular receptor FKBP12.[23][24] The FKBP12–rapamycin complex binds directly to the FKBP12-Rapamycin Binding (FRB) domain of mTOR, inhibiting its activity.[24]

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ Williams T, Tjian R (1991). "Characterization of a dimerization motif in AP-2 and its function in heterologous DNA-binding proteins". Science. 251 (4997): 1067–71. Bibcode:1991Sci...251.1067W. doi:10.1126/science.1998122. PMID 1998122.
  2. ↑ Williams T, Tjian R (1991). "Analysis of the DNA-binding and activation properties of the human transcription factor AP-2". Genes Dev. 5 (4): 670–82. doi:10.1101/gad.5.4.670. PMID 2010091.
  3. ↑ Hilger-Eversheim K, Moser M, Schorle H, Buettner R (2000). "Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control". Gene. 260 (1–2): 1–12. doi:10.1016/S0378-1119(00)00454-6. PMID 11137286.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 RefSeq (December 2009). "TFAP2A transcription factor AP-2 alpha [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  5. ↑ RefSeq (July 2008). "TFAP2B transcription factor AP-2 beta [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  6. ↑ RefSeq (July 2008). "TFAP2C transcription factor AP-2 gamma [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  7. ↑ HGNC (4 October 2020). "TFAP2D transcription factor AP-2 delta [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  8. ↑ HGNC (18 August 2020). "TFAP2C transcription factor AP-2 gamma [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  9. ↑ 9.0 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 Takayuki Murata, Chieko Noda, Yohei Narita1, Takahiro Watanabe, Masahiro Yoshida, Keiji Ashio, Yoshitaka Sato, Fumi Goshima, Teru Kanda, Hironori Yoshiyama, Tatsuya Tsurumi, and Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.
  10. ↑ 10.0 10.1 10.2 10.3 10.4 Isabelle R. Cohen, Susanne Grässel, Alan D. Murdoch, and Renat V. Iozzo (1 November 1993). "Structural characterization of the complete human perlecan gene and its promoter" (PDF). Proceedings of the National Academy of Sciences USA. 90 (21): 10404–10408. doi:10.1073/pnas.90.21.10404. PMID 8234307. Retrieved 6 September 2020.
  11. ↑ Vera M. Ripoll, Nicholas A. Meadows, Liza-Jane Raggatt, Ming K. Chang, Allison R. Pettit, Alan I. Cassady and David A. Hume (30 April 2005). "Microphthalmia transcription factor regulates the expression of the novel osteoclast factor GPNMB" (PDF). Gene. 413 (1–2): 32–41. doi:10.1016/j.gene.2008.01.014. Retrieved 18 March 2021.
  12. ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
  13. ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
  14. ↑ Z.G. E, Y.P. Zhang, J.H. Zhou and L. Wang (16 April 2014). "Roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137.
  15. ↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.
  16. ↑ 16.0 16.1 Kirk A. Staschke, Souvik Dey, John M. Zaborske, Lakshmi Reddy Palam, Jeanette N. McClintick, Tao Pan, Howard J. Edenberg, and Ronald C. Wek (May 28, 2010). "Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast" (PDF). The Journal of Biological Chemistry. 285 (22): 16893–16911. doi:10.1074/jbc.M110.121947. Retrieved 4 January 2021.
  17. ↑ Lisete Fernandes, Claudina Rodrigues-Pousada, Kevin Struhl (December 1997). "Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions". Molecular and Cellular Biology. 17 (12): 6982–6993. doi:10.1128/MCB.17.12.6982. Retrieved 11 March 2021.
  18. ↑ 18.0 18.1 18.2 18.3 18.4 18.5 18.6 Yao EF, Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
  19. ↑ Nicole Wagner, Kay-Dietrich Wagner, Heinz Theres, Christoph Englert, Andreas Schedl, and Holger Scholz (25 August 2005). "Coronary vessel development requires activation of the TrkB neurotrophin receptor by the Wilms' tumor transcription factor Wt1". Genes & Development. 19 (21): 2631–2642. doi:10.1101/gad.346405. Retrieved 26 September 2021.
  20. ↑ Wipperman MF, Montrose DC, Gotto AM, Hajjar DP (2019). "Mammalian Target of Rapamycin: A Metabolic Rheostat for Regulating Adipose Tissue Function and Cardiovascular Health". The American Journal of Pathology. 189 (3): 492–501. doi:10.1016/j.ajpath.2018.11.013. PMC 6412382. PMID 30803496.
  21. ↑ Beevers CS, Li F, Liu L, Huang S (August 2006). "Curcumin inhibits the mammalian target of rapamycin-mediated signaling pathways in cancer cells". International Journal of Cancer. 119 (4): 757–64. doi:10.1002/ijc.21932. PMID 16550606. Unknown parameter |s2cid= ignored (help)
  22. ↑ Kennedy BK, Lamming DW (June 2016). "The Mechanistic Target of Rapamycin: The Grand ConducTOR of Metabolism and Aging". Cell Metabolism. 23 (6): 990–1003. doi:10.1016/j.cmet.2016.05.009. PMC 4910876. PMID 27304501.
  23. ↑ Huang S, Houghton PJ (December 2001). "Mechanisms of resistance to rapamycins". Drug Resistance Updates. 4 (6): 378–91. doi:10.1054/drup.2002.0227. PMID 12030785.
  24. ↑ 24.0 24.1 Huang S, Bjornsti MA, Houghton PJ (2003). "Rapamycins: mechanism of action and cellular resistance". Cancer Biology & Therapy. 2 (3): 222–32. doi:10.4161/cbt.2.3.360. PMID 12878853.

External links


Retrieved from "https://www.wikidoc.org/index.php?title=Activating_protein_gene_transcriptions&oldid=1734017"