Rap1 regulatory factor gene transcriptions: Difference between revisions

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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.
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 SuccessablesRap1.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:
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:
# negative strand, negative direction, looking for ACCC(A/G)N(A/G)CA, 0.
# negative strand, negative direction, looking for ACCC(A/G)N(A/G)CA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for ACCC(A/G)N(A/G)CA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for ACCC(A/G)N(A/G)CA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for ACCC(A/G)N(A/G)CA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for TGGG(C/T)N(C/T)GT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TGGG(C/T)N(C/T)GT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TGGG(C/T)N(C/T)GT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TGGG(C/T)N(C/T)GT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TG(C/T)N(C/T)GGGT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TG(C/T)N(C/T)GGGT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TG(C/T)N(C/T)GGGT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TG(C/T)N(C/T)GGGT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
 
===Rap1 UTRs===
{{main|UTR promoter gene transcriptions}}
 
===Rap1 core promoters===
{{main|Core promoter gene transcriptions}}
 
===Rap1 proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===Rap1 distal promoters===
{{main|Distal promoter gene transcriptions}}


==See also==
==See also==

Revision as of 17:57, 19 February 2021

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]

"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.

See also

References

  1. ↑ 1.0 1.1 1.2 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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