Reb1 general regulatory factor gene transcriptions: Difference between revisions

Revision as of 01:52, 17 June 2021

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

Purified "Reb1 bound [...] exact TTACCCK occurrences [...] with >60% of 780 occurrences at promoters. [And can have] the extended motif VTTACCCGNH (IUPAC nomenclature) (Rhee and Pugh 2011)."^[1] K = G, T; V = not T, N - aNy base and H = not G.

Human genes

Consensus sequences

The apparent consensus sequence for Reb1 is 5'-TTACCC(G/T)-3'; however, an extended Reb1 has the consensus sequence 5'-ATTACCCGAA-3'.

Reb1 samplings

Copying the apparent consensus sequence for Reb1 TTACCC(G/T) and putting it in "⌘F" finds one located between ZSCAN22 or none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTACCC(G/T) (starting with SuccessablesREB.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 TTACCC(G/T), 1, TTACCCT at 3661.
positive strand, negative direction, looking for TTACCC(G/T), 0.
positive strand, positive direction, looking for TTACCC(G/T), 2, TTACCCT at 3170, TTACCCG at 2912.
negative strand, positive direction, looking for TTACCC(G/T), 0.
complement, negative strand, negative direction, looking for AATGGG(A/C), 0.
complement, positive strand, negative direction, looking for AATGGG(A/C), 1, ATGGGA at 3661.
complement, positive strand, positive direction, looking for AATGGG(A/C), 0.
complement, negative strand, positive direction, looking for AATGGG(A/C), 2, AATGGGA at 3170, AATGGGC at 2912.
inverse complement, negative strand, negative direction, looking for (A/C)GGGTAA, 0.
inverse complement, positive strand, negative direction, looking for (A/C)GGGTAA, 0.
inverse complement, positive strand, positive direction, looking for (A/C)GGGTAA, 0.
inverse complement, negative strand, positive direction, looking for (A/C)GGGTAA, 0.
inverse negative strand, negative direction, looking for (G/T)CCCATT, 0.
inverse positive strand, negative direction, looking for (G/T)CCCATT, 0.
inverse positive strand, positive direction, looking for (G/T)CCCATT, 0.
inverse negative strand, positive direction, looking for (G/T)CCCATT, 0.

REB UTRs

Negative strand, negative direction: TTACCCT at 3661.

REB distal promoters

Positive strand, positive direction: TTACCCT at 3170, TTACCCG at 2912.

Random dataset samplings

REBr0: 2, TTACCCG at 4135, TTACCCT at 1015.
REBr1: 2, TTACCCG at 4416, TTACCCG at 2965.
REBr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 1, TTACCCT at 4250.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Extended Reb1 samplings

An extended Reb1 (ATTACCCGAA) finds none located between ZSCAN22 or between ZNF497 and A1BG.

For the Basic programs testing consensus sequence ATTACCCGAA (starting with SuccessablesREBE.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 ATTACCCGAA, 0.
positive strand, negative direction, looking for ATTACCCGAA, 0.
positive strand, positive direction, looking for ATTACCCGAA, 0.
negative strand, positive direction, looking for ATTACCCGAA, 0.
complement, negative strand, negative direction, looking for TAATGGGCTT, 0.
complement, positive strand, negative direction, looking for TAATGGGCTT, 0.
complement, positive strand, positive direction, looking for TAATGGGCTT, 0.
complement, negative strand, positive direction, looking for TAATGGGCTT, 0.
inverse complement, negative strand, negative direction, looking for TTCGGGTAAT, 0.
inverse complement, positive strand, negative direction, looking for TTCGGGTAAT, 0.
inverse complement, positive strand, positive direction, looking for TTCGGGTAAT, 0.
inverse complement, negative strand, positive direction, looking for TTCGGGTAAT, 0.
inverse negative strand, negative direction, looking for AAGCCCATTA, 0.
inverse positive strand, negative direction, looking for AAGCCCATTA, 0.
inverse positive strand, positive direction, looking for AAGCCCATTA, 0.
inverse negative strand, positive direction, looking for AAGCCCATTA, 0.

Random dataset samplings

RDr0: 0.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Acknowledgements

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

References

↑ 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

[Rossi-1] 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.

[1]

@@ Line 63: / Line 63: @@
 # RDr7: 0.
 # RDr8: 0.
-# RDr9: 0.
+# RDr9: 1, TTACCCT at 4250.
 # RDr0ci: 0.
 # RDr1ci: 0.

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions

Reb1 general regulatory factor gene transcriptions: Difference between revisions

Revision as of 01:52, 17 June 2021

Contents

Human genes

Consensus sequences

Reb1 samplings

REB UTRs

REB distal promoters

Random dataset samplings

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Extended Reb1 samplings

Random dataset samplings

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Acknowledgements

See also

References

External links

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