The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro

Description

Description:	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog [Source:HGNC Symbol;Acc:HG
Entrez Summary	TBA
Ensembl ID:	ENSG00000134323
External Link:	T014207_1.02
Interpro	IPR002418; IPR011598; IPR012682; ;
Protein Domain:
Protein: ENSP00000281043	DBD: bHLH	Other: CENP-B_dimeris, LRS4, Myc_N

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific_DNA Binding_ PMIDS:17124508
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	a
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003700 sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000002
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
ChIP-seq	JASPAR		Inferred - Mycn (98% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Mycn (98% AA Identity, Mus musculus)

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 434, "endStyle": "curved", "aliStart": 382, "text": "HLH", "colour": "#2cb42c", "aliEnd": 434, "start": 382, "href": "http://pfam.xfam.org/family/PF00010.24", "type": "pfama", "display": "true", "metadata": {"end": 434, "description": "A number of eukaryotic proteins, which probably are sequence specific DNA-binding proteins that act as transcription factors, share a conserved domain of 40 to 50 amino acid residues. It has been proposed [PUBMED:2493990] that this domain is formed of two amphipathic helices joined by a variable length linker region that could form a loop. This 'helix-loop-helix' (HLH) domain mediates protein dimerization and has been found in the proteins listed below [PUBMED:1521738]. Most of these proteins have an extra basic region of about 15 amino acid residues that is adjacent to the HLH domain and specifically binds to DNA. They are refered as basic helix-loop-helix proteins (bHLH), and are classified in two groups: class A (ubiquitous) and class B (tissue-specific). Members of the bHLH family bind variations on the core sequence 'CANNTG', also refered to as the E-box motif. The homo- or heterodimerization mediated by the HLH domain is independent of, but necessary for DNA binding, as two basic regions are required for DNA binding activity. The HLH proteins lacking the basic domain (Emc, Id) function as negative regulators, since they form heterodimers, but fail to bind DNA. The hairy-related proteins (hairy, E(spl), deadpan) also repress transcription although they can bind DNA. The proteins of this subfamily act together with co-repressor proteins, like groucho, through their C-terminal motif WRPW.", "database": "PfamA", "aliStart": 382, "scoreName": "E-value", "accession": "PF00010.24", "start": 382, "score": 1.3e-15, "identifier": "Helix-loop-helix DNA-binding domain", "type": "DBD", "aliEnd": 434}}, {"startStyle": "straight", "end": 372, "endStyle": "straight", "aliStart": 9, "text": "Myc_N", "colour": "#9999ff", "aliEnd": 372, "start": 9, "href": "http://pfam.xfam.org/family/PF01056.16", "type": "pfama", "display": "true", "metadata": {"end": 372, "description": "The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see Pfam:PF00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication [2]. Mutations in the C-terminal 20 residues of this domain cause unique changes in the induction of apoptosis, transformation, and G2 arrest [3].", "database": "PfamA", "aliStart": 9, "scoreName": "E-value", "accession": "PF01056.16", "start": 9, "score": 3.599999999999999e-147, "identifier": "Myc amino-terminal region", "type": "DBD", "aliEnd": 372}}, {"startStyle": "straight", "end": 333, "endStyle": "jagged", "aliStart": 254, "text": "CENP-B_dimeris", "colour": "#9999ff", "aliEnd": 278, "start": 248, "href": "http://pfam.xfam.org/family/PF09026.8", "type": "pfama", "display": "true", "metadata": {"end": 333, "description": "The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation [1].", "database": "PfamA", "aliStart": 254, "scoreName": "E-value", "accession": "PF09026.8", "start": 248, "score": 0.0025, "identifier": "Centromere protein B dimerisation domain", "type": "DBD", "aliEnd": 278}}, {"startStyle": "jagged", "end": 298, "endStyle": "straight", "aliStart": 233, "text": "LRS4", "colour": "#9999ff", "aliEnd": 292, "start": 217, "href": "http://pfam.xfam.org/family/PF10422.7", "type": "pfama", "display": "true", "metadata": {"end": 298, "description": "Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I [1][3]. The orthologous complex in Schizosaccharomyces pombe is not required for meiosis I chromosome segregation, but is proposed to play a similar physiological role in clamping microtubule binding sites [2].  In S .cerevisiae this subunit is called LRS4, and in S. pombe it is known as Mde4.", "database": "PfamA", "aliStart": 233, "scoreName": "E-value", "accession": "PF10422.7", "start": 217, "score": 0.0082, "identifier": "Monopolin complex subunit LRS4", "type": "DBD", "aliEnd": 292}}], "length": 465}

TF Info Page for MYCN (bHLH)