Abf1 regulatory factor gene transcriptions: Difference between revisions

Revision as of 19:10, 5 June 2021

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

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."^[1]

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).^[2]

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.

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 5'-CGTNNNNN(A/G)(C/T)GA(C/T)-3' (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 regulatory factor distal promoters

Positive strand, negative direction: 5'-CGTTCTTTATGAT-3' at 352 and complement.

Positive strand, positive direction: 5'-CGTCACCGGTGAC-3' at 2073, 5'-CGTTCGGTGTGAC-3' at 346 and complements.

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: 0.
Abfmr1ci: 0.
Abfmr2ci: 0.
Abfmr3ci: 1, CGTGTAGTGTGAC at 2207.
Abfmr4ci: 0.
Abfmr5ci: 0.
Abfmr6ci: 0.
Abfmr7ci: 0.
Abfmr8ci: 0.
Abfmr9ci: 0.

Abfmr UTRs

Abfmr core promoters

Abfmr proximal promoters

Abfmr distal promoters

Acknowledgements

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

References

↑ RefSeq (July 2008). "MSC musculin [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 10 October 2020.
↑ 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

[RefSeq9242-1] RefSeq (July 2008). "MSC musculin [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 10 October 2020.

[Rossi-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.

[1]

[2]

@@ Line 96: / Line 96: @@
 # Abfmr1ci: 0.
 # Abfmr2ci: 0.
-# Abfmr3ci: 0.
+# Abfmr3ci: 1, CGTGTAGTGTGAC at 2207.
 # Abfmr4ci: 0.
 # Abfmr5ci: 0.

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B 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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene 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 Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene 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