Rap1 regulatory factor gene transcriptions: Difference between revisions

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# inverse positive strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse positive strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse negative strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
# inverse negative strand, positive direction, looking for AC(A/G)N(A/G)CCCA, 0.
==Rap1 prevalent samplings==
{{main|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:
# negative strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
===RAPP UTRs===
{{main|UTR promoter gene transcriptions}}
===RAPP core promoters===
{{main|Core promoter gene transcriptions}}
===RAPP proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===RAPP distal promoters===
{{main|Distal promoter gene transcriptions}}
==Acknowledgements==
The content on this page was first contributed by: Henry A. Hoff.


==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
{{Div col end}}
{{Div col end}}


Revision as of 18:37, 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]

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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

RAPP UTRs

Main article: UTR promoter gene transcriptions

RAPP core promoters

Main article: Core promoter gene transcriptions

RAPP proximal promoters

Main article: Proximal promoter gene transcriptions

RAPP 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

Retrieved from "https://www.wikidoc.org/index.php?title=Rap1_regulatory_factor_gene_transcriptions&oldid=1690815"