Mcm1 regulatory factor gene transcriptions

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

Human genes

Interactions

Consensus sequences

Consensus sequences: NN(A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T)NNN.^[1]

The primary consensus sequence is apparently TT(A/T)CCNN(A/T)TNGG(A/T)AA.^[1]

A "subset of bound and unbound motif occurrences [...] contained all of the most highly conserved nucleotides of the 16-bp pseudosymmetric motif (TTnCCnnnTnnGGnAA) ([...] Shore and Sharrocks 1995; Hughes and de Boer 2013)."^[1]

Samplings

Copying a consensus regulatory element: TT(A/T)CCNN(A/T)TNGG(A/T)AA and putting the sequence in "⌘F" finds no locations for this sequence in any A1BG direction as can be found by the computer programs.

For the Basic programs testing consensus sequence TT(A/T)CCNN(A/T)TNGG(A/T)AA (starting with SuccessablesMcm.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 TT(A/T)CCNN(A/T)TNGG(A/T)AA, 0.
positive strand, negative direction, looking for TT(A/T)CCNN(A/T)TNGG(A/T)AA, 0.
positive strand, positive direction, looking for TT(A/T)CCNN(A/T)TNGG(A/T)AA, 0.
negative strand, positive direction, looking for TT(A/T)CCNN(A/T)TNGG(A/T)AA, 0.
complement, negative strand, negative direction, looking for AA(A/T)GGNN(A/T)ANCC(A/T)TT, 0.
complement, positive strand, negative direction, looking for AA(A/T)GGNN(A/T)ANCC(A/T)TT, 0.
complement, positive strand, positive direction, looking for AA(A/T)GGNN(A/T)ANCC(A/T)TT, 0.
complement, negative strand, positive direction, looking for AA(A/T)GGNN(A/T)ANCC(A/T)TT, 0.
inverse complement, negative strand, negative direction, looking for TT(A/T)CCNA(A/T)NNGG(A/T)AA, 0.
inverse complement, positive strand, negative direction, looking for TT(A/T)CCNA(A/T)NNGG(A/T)AA, 0.
inverse complement, positive strand, positive direction, looking for TT(A/T)CCNA(A/T)NNGG(A/T)AA, 0.
inverse complement, negative strand, positive direction, looking for TT(A/T)CCNA(A/T)NNGG(A/T)AA, 0.
inverse negative strand, negative direction, looking for AA(A/T)GGNT(A/T)NNCC(A/T)TT, 0.
inverse positive strand, negative direction, looking for AA(A/T)GGNT(A/T)NNCC(A/T)TT, 0.
inverse positive strand, positive direction, looking for AA(A/T)GGNT(A/T)NNCC(A/T)TT, 0.
inverse negative strand, positive direction, looking for AA(A/T)GGNT(A/T)NNCC(A/T)TT, 0.

Rossi samplings

Copying a responsive elements consensus sequence TTnCCnnnTnnGGnAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTnCCnnnTnnGGnAA (starting with SuccessablesMcmR.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 TTNCCNNNTNNGGNAA, 0.
positive strand, negative direction, looking for TTNCCNNNTNNGGNAA, 0.
positive strand, positive direction, looking for TTNCCNNNTNNGGNAA, 0.
negative strand, positive direction, looking for TTNCCNNNTNNGGNAA, 0.
inverse complement, negative strand, negative direction, looking for TTNCCNNANNNGGNAA, 0.
inverse complement, positive strand, negative direction, looking for TTNCCNNANNNGGNAA, 0.
inverse complement, positive strand, positive direction, looking for TTNCCNNANNNGGNAA, 0.
inverse complement, negative strand, positive direction, looking for TTNCCNNANNNGGNAA, 0.

McmR random dataset samplings

McmRr0: 0.
McmRr1: 0.
McmRr2: 0.
McmRr3: 0.
McmRr4: 0.
McmRr5: 0.
McmRr6: 0.
McmRr7: 0.
McmRr8: 0.
McmRr9: 0.
McmRr0ci: 0.
McmRr1ci: 0.
McmRr2ci: 0.
McmRr3ci: 0.
McmRr4ci: 0.
McmRr5ci: 0.
McmRr6ci: 0.
McmRr7ci: 0.
McmRr8ci: 0.
McmRr9ci: 0.

References

↑ ^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

[Rossi-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.

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