Abf1 regulatory factor gene transcriptions

# Human genes
Gene ID: 9242 is MSC musculin on 8q13.3 aka ABF1; MYOR; ABF-1; bHLHa22: "The protein encoded by this gene is a transcriptional repressor capable of binding an E-box element either as a homodimer or as a heterodimer with E2A in vitro. The encoded protein also forms heterodimers with E2A proteins in vivo. This protein is capable of inhibiting the transactivation capability of E47, an E2A protein, in mammalian cells. This gene is a downstream target of the B-cell receptor signal transduction pathway."

# Consensus sequences
Specific "sequences considered as exact Abf1 motif occurrences": CGTNNNNNACGA(C/T), CGTNNNNNA(C/T)GAC, CGTNNNNNA(C/T)GA(C/T), CGTNNNNN(A/G)(C/T)GA(C/T) (Abfm).

# Hypotheses
- A1BG has no Abf1 regulatory factors in either promoter.
- A1BG is not transcribed by an Abf1 regulatory factor.
- Abf1 regulatory factor does not participate in the transcription of A1BG.

# Abf1 samplings
Copying a consensus Abf1 regulatory factor: 5'-CGTCCTCTACG-3' and putting the sequence in "F" locates none between ZSCAN22 to A1BG direction, and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence 5'-CGTNNNNNACGAT-3' (starting with SuccessablesAbf1.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbf1--.bas, looking for 5'-CGTNNNNNACGAT-3', 0.
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbf1-+.bas, looking for 5'-CGTNNNNNACGAT-3', 0.
- positive strand, negative direction is SuccessablesAbf1+-.bas, looking for 5'-CGTNNNNNACGAT-3', 0.
- positive strand, positive direction is SuccessablesAbf1++.bas, looking for 5'-CGTNNNNNACGAT-3', 0.
- complement, negative strand, negative direction is SuccessablesAbf1c--.bas, looking for 5'-GCANNNNNTGCTA-3', 0.
- complement, negative strand, positive direction is SuccessablesAbf1c-+.bas, looking for 5'-GCANNNNNTGCTA-3', 0.
- complement, positive strand, negative direction is SuccessablesAbf1c+-.bas, looking for 5'-GCANNNNNTGCTA-3', 0.
- complement, positive strand, positive direction is SuccessablesAbf1c++.bas, looking for 5'-GCANNNNNTGCTA-3', 0.
- inverse complement, negative strand, negative direction is SuccessablesAbf1ci--.bas, looking for 5'-ATCGTNNNNNACG-3', 0.
- inverse complement, negative strand, positive direction is SuccessablesAbf1ci-+.bas, looking for 5'-ATCGTNNNNNACG-3', 0.
- inverse complement, positive strand, negative direction is SuccessablesAbf1ci+-.bas, looking for 5'-ATCGTNNNNNACG-3', 0.
- inverse complement, positive strand, positive direction is SuccessablesAbf1ci++.bas, looking for 5'-ATCGTNNNNNACG-3', 0.
- inverse negative strand, negative direction is SuccessablesAbf1i--.bas, looking for 5'-TAGCANNNNNTGC-3', 0.
- inverse negative strand, positive direction is SuccessablesAbf1i-+.bas, looking for 5'-TAGCANNNNNTGC-3', 0.
- inverse positive strand, negative direction is SuccessablesAbf1i+-.bas, looking for 5'-TAGCANNNNNTGC-3', 0.
- inverse positive strand, positive direction is SuccessablesAbf1i++.bas, looking for 5'-TAGCANNNNNTGC-3', 0.
For the Basic programs testing consensus sequence CGTNNNNN(A/G)(C/T)GA(C/T) (starting with SuccessablesAbfm.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 is SuccessablesAbfm--.bas, looking for 5'-CGTNNNNN(A/G)(C/T)GA(C/T)-3', 0.
- negative strand, positive direction is SuccessablesAbfm-+.bas, looking for 5'-CGTNNNNN(A/G)(C/T)GA(C/T)-3', 0.
- positive strand, negative direction is SuccessablesAbfm+-.bas, looking for 5'-CGTNNNNN(A/G)(C/T)GA(C/T)-3', 1, 5'-CGTTCTTTATGAT-3' at 352.
- positive strand, positive direction is SuccessablesAbfm++.bas, looking for 5'-CGTNNNNN(A/G)(C/T)GA(C/T)-3', 2, 5'-CGTTCGGTGTGAC-3' at 346, 5'-CGTCACCGGTGAC-3' at 2073.
- complement, negative strand, negative direction is SuccessablesAbfmc--.bas, looking for 5'-GCANNNNN(C/T)(A/G)CT(A/G)-3', 1, 5'-GCAAGAAATACTA-3' at 352.
- complement, negative strand, positive direction is SuccessablesAbfmc-+.bas, looking for 5'-GCANNNNN(C/T)(A/G)CT(A/G)-3', 2, 5'-GCAAGCCACACTG-3' at 346, 5'-GCAGTGGCCACTG-3' at 2073.
- complement, positive strand, negative direction is SuccessablesAbfmc+-.bas, looking for 5'-GCANNNNN(C/T)(A/G)CT(A/G)-3', 0.
- complement, positive strand, positive direction is SuccessablesAbfmc++.bas, looking for 5'-GCANNNNN(C/T)(A/G)CT(A/G)-3', 0.
- inverse complement, negative strand, negative direction is SuccessablesAbfmci--.bas, looking for 5'-(A/G)TC(A/G)(C/T)NNNNNACG-3', 0.
- inverse complement, negative strand, positive direction is SuccessablesAbfmci-+.bas, looking for 5'-(A/G)TC(A/G)(C/T)NNNNNACG-3', 0.
- inverse complement, positive strand, negative direction is SuccessablesAbfmci+-.bas, looking for 5'-(A/G)TC(A/G)(C/T)NNNNNACG-3', 0.
- inverse complement, positive strand, positive direction is SuccessablesAbfmci++.bas, looking for 5'-(A/G)TC(A/G)(C/T)NNNNNACG-3', 0.
- inverse negative strand, negative direction is SuccessablesAbfmi--.bas, looking for 5'-(C/T)AG(C/T)(A/G)NNNNNTGC-3', 0.
- inverse negative strand, positive direction is SuccessablesAbfmi-+.bas, looking for 5'-(C/T)AG(C/T)(A/G)NNNNNTGC-3', 0.
- inverse positive strand, negative direction is SuccessablesAbfmi+-.bas, looking for 5'-(C/T)AG(C/T)(A/G)NNNNNTGC-3', 0.
- inverse positive strand, positive direction is SuccessablesAbfmi++.bas, looking for 5'-(C/T)AG(C/T)(A/G)NNNNNTGC-3', 0.

## Abfm negative direction (2596-1) distal promoters
- Positive strand, negative direction: CGTTCTTTATGAT at 352.

## Abfm positive direction (4050-1) distal promoters
- Positive strand, positive direction: CGTCACCGGTGAC at 2073, CGTTCGGTGTGAC at 346.

# Abfm random dataset samplings
- Abfmr0: 0.
- Abfmr1: 0.
- Abfmr2: 0.
- Abfmr3: 1, CGTGTAGTGTGAC at 2207.
- Abfmr4: 0.
- Abfmr5: 0.
- Abfmr6: 1, CGTGTCATGTGAC at 1344.
- Abfmr7: 0.
- Abfmr8: 0.
- Abfmr9: 0.
- Abfmr0ci: 1, GTCATATCGTACG at 3968.
- Abfmr1ci: 0.
- Abfmr2ci: 1, ATCGCATTAAACG at 2757.
- Abfmr3ci: 0.
- Abfmr4ci: 0.
- Abfmr5ci: 0.
- Abfmr6ci: 0.
- Abfmr7ci: 0.
- Abfmr8ci: 0.
- Abfmr9ci: 0.

## Abfmr arbitrary (evens) (4560-2846) UTRs
- Abfmr0ci: GTCATATCGTACG at 3968.

## Abfmr arbitrary negative direction (evens) (2811-2596) proximal promoters
- Abfmr2ci: ATCGCATTAAACG at 2757.

## Abfmr arbitrary negative direction (evens) (2596-1) distal promoters
- Abfmr6: CGTGTCATGTGAC at 1344.

## Abfmr alternate negative direction (odds) (2596-1) distal promoters
- Abfmr3: CGTGTAGTGTGAC at 2207.

## Abfmr arbitrary positive direction (odds) (4050-1) distal promoters
- Abfmr3: CGTGTAGTGTGAC at 2207.

## Abfmr alternate positive direction (evens) (4050-1) distal promoters
- Abfmr6: CGTGTCATGTGAC at 1344.
- Abfmr0ci: GTCATATCGTACG at 3968.
- Abfmr2ci: ATCGCATTAAACG at 2757.

# Discussion
The general consensus sequence for Abfm CGTNNNNN(A/G)(C/T)GA(C/T) occurs on both sides of A1BG but only in the distal promoters. Random datasets, even numbered arbitrarily assigned to the negative direction and odd numbered assigned to the positive direction yielded a sequence in the UTR, core promoter and distal promoter for the negative direction and a sequence in the distal promoter for the positive direction. The real consensus sequence yielded only three results: one in the negative direction and two in the positive, all in the distal promoters. The random sequences (four total) occurred in the UTR, proximal promoter and distal promoter for the negative direction and one in the distal promoter for the positive direction. While the differences between real and random are small (three vs. four), (all distal vs. UTR, proximal and two distal), they are likely significant as the random datasets (10) should have encompassed the real (2, each side of A1BG) but this did not occur.

# Abfm analysis and results
Specific "sequences considered as exact Abf1 motif occurrences": CGTNNNNNACGA(C/T), CGTNNNNNA(C/T)GAC, CGTNNNNNA(C/T)GA(C/T), CGTNNNNN(A/G)(C/T)GA(C/T) (Abfm).
Comparison:
The occurrences of real Abfms are greater than the randoms. This suggests that the real Abfms are likely active or activable.

# B-cell receptor signal transduction pathway

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