The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	2 Obligate heteromer	In vivo/Misc source		Obligate heterotrimer of NFYA, NFYB, and NFYC

Description

Description:	nuclear transcription factor Y subunit beta [Source:HGNC Symbol;Acc:HGNC:7805]
Entrez Summary	TBA
Ensembl ID:	ENSG00000120837
External Link:	T153691_1.02
Interpro	IPR003956; IPR003958; IPR009072; ;
Protein Domain:
Protein: ENSP00000240055	DBD: Other	Other: CBFD_NFYB_HMF, CENP-T_C, Histone, TFIID-18kDa
Protein: ENSP00000448250	DBD: Other	Other: CBFD_NFYB_HMF, CENP-T_C, Histone, TFIID-18kDa
Protein: ENSP00000447486	DBD: Other	Other: CBFD_NFYB_HMF, CENP-T_C, Histone, TFIID-18kDa

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_Basal Transcription Factor_TF PPI_ PMIDS:12401788
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:0000019
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	Obligate_Multimer

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
ChIP-seq	JASPAR		Direct
Misc	HocoMoco		Direct

Structure

Structure	PDB	4AWL

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

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{"regions": [{"startStyle": "straight", "end": 123, "endStyle": "straight", "aliStart": 59, "text": "CBFD_NFYB_HMF", "colour": "#9999ff", "aliEnd": 123, "start": 58, "href": "http://pfam.xfam.org/family/PF00808.21", "type": "pfama", "display": "true", "metadata": {"end": 123, "description": "This family includes archaebacterial histones and histone like transcription factors from eukaryotes.", "database": "PfamA", "aliStart": 59, "scoreName": "E-value", "accession": "PF00808.21", "start": 58, "score": 1.7000000000000001e-29, "identifier": "Histone-like transcription factor (CBF/NF-Y) and archaeal histone", "type": "DBD", "aliEnd": 123}}, {"startStyle": "jagged", "end": 125, "endStyle": "straight", "aliStart": 56, "text": "Histone", "colour": "#9999ff", "aliEnd": 123, "start": 27, "href": "http://pfam.xfam.org/family/PF00125.22", "type": "pfama", "display": "true", "metadata": {"end": 125, "description": NaN, "database": "PfamA", "aliStart": 56, "scoreName": "E-value", "accession": "PF00125.22", "start": 27, "score": 4.6e-06, "identifier": "Core histone H2A/H2B/H3/H4", "type": "DBD", "aliEnd": 123}}, {"startStyle": "jagged", "end": 125, "endStyle": "jagged", "aliStart": 82, "text": "TFIID-18kDa", "colour": "#9999ff", "aliEnd": 123, "start": 68, "href": "http://pfam.xfam.org/family/PF02269.14", "type": "pfama", "display": "true", "metadata": {"end": 125, "description": "This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [1]", "database": "PfamA", "aliStart": 82, "scoreName": "E-value", "accession": "PF02269.14", "start": 68, "score": 0.00073, "identifier": "Transcription initiation factor IID, 18kD subunit", "type": "DBD", "aliEnd": 123}}, {"startStyle": "straight", "end": 127, "endStyle": "jagged", "aliStart": 58, "text": "CENP-T_C", "colour": "#9999ff", "aliEnd": 123, "start": 53, "href": "http://pfam.xfam.org/family/PF15511.4", "type": "pfama", "display": "true", "metadata": {"end": 127, "description": "CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore.  Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure.  The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].", "database": "PfamA", "aliStart": 58, "scoreName": "E-value", "accession": "PF15511.4", "start": 53, "score": 0.0008900000000000001, "identifier": "Centromere kinetochore component CENP-T histone fold", "type": "DBD", "aliEnd": 123}}], "length": 131}

TF Info Page for NFYB (Unknown)