Rap1 regulatory factor gene transcriptions

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

"Rap1 is another GRF that organizes chromatin, binds promoters of genes that encode ribosomal and glycolytic proteins, and binds telomeres (Shore 1994; Ganapathi et al. 2011; Hughes and de Boer 2013). [...] DNA shape analysis revealed that Rap1 motifs possess an intrinsically wide minor groove spanning the central degenerate region of the motif that was wider at binding-competent sites [...]. A clear trend was observed between increased width of the minor groove in the central degenerate region of the motif and increased Rap1 binding in vitro."[1]

Human genes

Consensus sequences

Consensus sequences: C(A/C/G)(A/C/G)(A/G)(C/G/T)C(A/C/T)(A/G/T)(C/G/T)(A/G/T)(A/C/G)(A/C)(A/C/T)(A/C/T).[1]

Reduced consensus sequence including more frequent nucleotides: (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C).[1]

"When the core DNA sequence of the Rap1 motif [...] was held constant (ACCCRnRCA), less than half of the sites were detectably bound [...]."[1]

Rap1 samplings

Copying an apparent consensus sequence for Rap1 (CCCACCAACAAAA) and putting it in "⌘F" finds none located between ZSCAN22 or none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ACCC(A/G)N(A/G)CA (starting with SuccessablesRAP.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 ACCC(A/G)N(A/G)CA, 0.
  2. positive strand, negative direction, looking for ACCC(A/G)N(A/G)CA, 0.
  3. positive strand, positive direction, looking for ACCC(A/G)N(A/G)CA, 0.
  4. negative strand, positive direction, looking for ACCC(A/G)N(A/G)CA, 0.
  5. complement, negative strand, negative direction, looking for TGGG(C/T)N(C/T)GT, 0.
  6. complement, positive strand, negative direction, looking for TGGG(C/T)N(C/T)GT, 0.
  7. complement, positive strand, positive direction, looking for TGGG(C/T)N(C/T)GT, 0.
  8. complement, negative strand, positive direction, looking for TGGG(C/T)N(C/T)GT, 0.
  9. inverse complement, negative strand, negative direction, looking for TG(C/T)N(C/T)GGGT, 0.
  10. inverse complement, positive strand, negative direction, looking for TG(C/T)N(C/T)GGGT, 0.
  11. inverse complement, positive strand, positive direction, looking for TG(C/T)N(C/T)GGGT, 0.
  12. inverse complement, negative strand, positive direction, looking for TG(C/T)N(C/T)GGGT, 0.
  13. inverse negative strand, negative direction, looking for AC(A/G)N(A/G)CCCA, 0.
  14. inverse positive strand, negative direction, looking for AC(A/G)N(A/G)CCCA, 0.
  15. inverse positive strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
  16. inverse negative strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.

Rap1 prevalent samplings

Main article: Model samplings

For the Basic programs testing consensus sequence (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C) (starting with SuccessablesRAPP.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 (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C), 0.
  2. positive strand, negative direction, looking for (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C), 0.
  3. positive strand, positive direction, looking for (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C), 1, GAACCCACACCTC at 1807.
  4. negative strand, positive direction, looking for (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C), 0.
  5. complement, negative strand, negative direction, looking for (C/T)(G/T)TGGG(C/T)N(C/T)G(G/T)(A/G)(G/T), 0.
  6. complement, positive strand, negative direction, looking for (C/T)(G/T)TGGG(C/T)N(C/T)G(G/T)(A/G)(G/T), 0.
  7. complement, positive strand, positive direction, looking for (C/T)(G/T)TGGG(C/T)N(C/T)G(G/T)(A/G)(G/T), 0.
  8. complement, negative strand, positive direction, looking for (C/T)(G/T)TGGG(C/T)N(C/T)G(G/T)(A/G)(G/T), 1, CTTGGGTGTGGAG at 1807.
  9. inverse complement, negative strand, negative direction, looking for (G/T)(A/G)(G/T)G(C/T)N(C/T)GGGT(G/T)(C/T), 0.
  10. inverse complement, positive strand, negative direction, looking for (G/T)(A/G)(G/T)G(C/T)N(C/T)GGGT(G/T)(C/T), 0.
  11. inverse complement, positive strand, positive direction, looking for (G/T)(A/G)(G/T)G(C/T)N(C/T)GGGT(G/T)(C/T), 0.
  12. inverse complement, negative strand, positive direction, looking for (G/T)(A/G)(G/T)G(C/T)N(C/T)GGGT(G/T)(C/T), 0.
  13. inverse negative strand, negative direction, looking for (A/C)(C/T)(A/C)C(A/G)N(A/G)CCCA(A/C)(A/G), 0.
  14. inverse positive strand, negative direction, looking for (A/C)(C/T)(A/C)C(A/G)N(A/G)CCCA(A/C)(A/G), 0.
  15. inverse positive strand, positive direction, looking for (A/C)(C/T)(A/C)C(A/G)N(A/G)CCCA(A/C)(A/G), 0.
  16. inverse negative strand, positive direction, looking for (A/C)(C/T)(A/C)C(A/G)N(A/G)CCCA(A/C)(A/G), 0.

RAPP distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: GAACCCACACCTC at 1807.

Random dataset samplings

  1. Rappr0: 0.
  2. Rappr1: 0.
  3. Rappr2: 0.
  4. Rappr3: 0.
  5. Rappr4: 0.
  6. Rappr5: 0.
  7. Rappr6: 0.
  8. Rappr7: 0.
  9. Rappr8: 0.
  10. Rappr9: 0.
  11. Rappr0ci: 0.
  12. Rappr1ci: 0.
  13. Rappr2ci: 0.
  14. Rappr3ci: 0.
  15. Rappr4ci: 0.
  16. Rappr5ci: 0.
  17. Rappr6ci: 0.
  18. Rappr7ci: 0.
  19. Rappr8ci: 0.
  20. Rappr9ci: 0.

Rappr UTRs

Main article: UTR promoter gene transcriptions

Rappr core promoters

Main article: Core promoter gene transcriptions

Rappr proximal promoters

Main article: Proximal promoter gene transcriptions

Rappr distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.

External links

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