Reb1 general regulatory factor gene transcriptions

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.
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.

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.
REBr3: 0.
REBr4: 0.
REBr5: 0.
REBr6: 0.
REBr7: 0.
REBr8: 0.
REBr9: 1, TTACCCT at 4250.
REBr0ci: 2, CGGGTAA at 973, AGGGTAA at 321.
REBr1ci: 1, CGGGTAA at 1815.
REBr2ci: 2, CGGGTAA at 3979, AGGGTAA at 3112.
REBr3ci: 1, AGGGTAA at 1812.
REBr4ci: 1, AGGGTAA at 1210.
REBr5ci: 0.
REBr6ci: 1, AGGGTAA at 399.
REBr7ci: 0.
REBr8ci: 0.
REBr9ci: 1, AGGGTAA at 1107.

REBr UTRs

REBr0: TTACCCG at 4135.
REBr2ci: CGGGTAA at 3979, AGGGTAA at 3112.

REBr core promoters

REBr1: TTACCCG at 4416.

REBr proximal promoters

REBr9: TTACCCT at 4250.

REBr distal promoters

REBr0: TTACCCT at 1015.
REBr0ci: CGGGTAA at 973, AGGGTAA at 321.
REBr4ci: 1, AGGGTAA at 1210.
REBr6ci: 1, AGGGTAA at 399.

REBr1: TTACCCG at 2965.
REBr1ci: CGGGTAA at 1815.
REBr3ci: AGGGTAA at 1812.
REBr9ci: AGGGTAA at 1107.

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.

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Reb1 general regulatory factor gene transcriptions

Contents

Human genes

Consensus sequences

Reb1 samplings

REB UTRs

REB distal promoters

Random dataset samplings

REBr UTRs

REBr core promoters

REBr proximal promoters

REBr 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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