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.
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.

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.

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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