Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Likely to be sequence specific TF
3 Low specificity DNA-binding protein
No motif
Contains an archaeal histone-like fold (CBF_NFY). but at best would have low sequence specificity. Known role in centromere assembly and lack of known sequence specificity suggest that it is unlikely to be a sequence specific TF.
Description
Description:
centromere protein T [Source:HGNC Symbol;Acc:HGNC:25787]
Entrez Summary
#!usr/local/bin/perl
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The centromere is a specialized chromatin domain, present
throughout the cell cycle, that acts as a platform on which the transient
assembly of the kinetochore occurs during mitosis. All active centromeres are
characterized by the presence of long arrays of nucleosomes in which CENPA
(MIM 117139) replaces histone H3 (see MIM 601128). CENPT is an additional
factor required for centromere assembly (Foltz et al., 2006 [PubMed
16622419]).[supplied by OMIM, Mar 2008]
Ensembl ID:
ENSG00000102901
External Link:
CisBP
Interpro
IPR009072 ; ;
Protein Domain:
ENSP00000400140
Protein Domain:
ENSP00000457810
Domain:
Protein: ENSP00000400140DBD: OtherOther: Bromo_TP, CBFD_NFYB_HMF, CENP-S, CENP-T_C, CENP-T_Protein: ENSP00000457810DBD: OtherOther: Bromo_TP, CBFD_NFYB_HMF, CENP-S, CENP-T_C, CENP-T_
Previous Annotations
Source
Annotation
TF-CAT classification
No PMIDS:
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.
c
CisBP considers it as a TF?
No
TFclass considers it as a TF?
No
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"
No
GO-Info
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
5a, one of the source datasets predicts is as a TF
TF has conditional DNA-binding requirements
DNA-Binding
Published Motif Data
Structure
Experimental History
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{"regions": [{"startStyle": "straight", "end": 415, "endStyle": "straight", "aliStart": 1, "text": "CENP-T_N", "colour": "#9999ff", "aliEnd": 415, "start": 1, "href": "http://pfam.xfam.org/family/PF16171.3", "type": "pfama", "display": "true", "metadata": {"end": 415, "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 family represents the N-terminus of CENP-T [1-3].", "database": "PfamA", "aliStart": 1, "scoreName": "E-value", "accession": "PF16171.3", "start": 1, "score": 4.899999999999998e-185, "identifier": "Centromere kinetochore component CENP-T N-terminus", "type": "DBD", "aliEnd": 415}}, {"startStyle": "straight", "end": 553, "endStyle": "straight", "aliStart": 452, "text": "CENP-T_C", "colour": "#9999ff", "aliEnd": 551, "start": 450, "href": "http://pfam.xfam.org/family/PF15511.4", "type": "pfama", "display": "true", "metadata": {"end": 553, "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": 452, "scoreName": "E-value", "accession": "PF15511.4", "start": 450, "score": 5.5e-36, "identifier": "Centromere kinetochore component CENP-T histone fold", "type": "DBD", "aliEnd": 551}}, {"startStyle": "jagged", "end": 525, "endStyle": "straight", "aliStart": 489, "text": "CENP-S", "colour": "#9999ff", "aliEnd": 522, "start": 470, "href": "http://pfam.xfam.org/family/PF15630.4", "type": "pfama", "display": "true", "metadata": {"end": 525, "description": "CENP-S is a family of vertebral and fungal kinetochore component proteins. CENP-S complexes with CENP-X to form a stable CENP-T-W-S-X heterotetramer.", "database": "PfamA", "aliStart": 489, "scoreName": "E-value", "accession": "PF15630.4", "start": 470, "score": 3e-09, "identifier": "CENP-S protein", "type": "DBD", "aliEnd": 522}}, {"startStyle": "jagged", "end": 519, "endStyle": "straight", "aliStart": 477, "text": "CBFD_NFYB_HMF", "colour": "#9999ff", "aliEnd": 517, "start": 471, "href": "http://pfam.xfam.org/family/PF00808.21", "type": "pfama", "display": "true", "metadata": {"end": 519, "description": "This family includes archaebacterial histones and histone like transcription factors from eukaryotes.", "database": "PfamA", "aliStart": 477, "scoreName": "E-value", "accession": "PF00808.21", "start": 471, "score": 0.0015, "identifier": "Histone-like transcription factor (CBF/NF-Y) and archaeal histone", "type": "DBD", "aliEnd": 517}}, {"startStyle": "jagged", "end": 528, "endStyle": "straight", "aliStart": 476, "text": "Bromo_TP", "colour": "#9999ff", "aliEnd": 524, "start": 474, "href": "http://pfam.xfam.org/family/PF07524.11", "type": "pfama", "display": "true", "metadata": {"end": 528, "description": "This domain is predicted to bind DNA [1] and is often found associated with Pfam:PF00439 and in transcription factors. It has a histone-like fold.", "database": "PfamA", "aliStart": 476, "scoreName": "E-value", "accession": "PF07524.11", "start": 474, "score": 0.0019, "identifier": "Bromodomain associated", "type": "DBD", "aliEnd": 524}}, {"startStyle": "jagged", "end": 522, "endStyle": "straight", "aliStart": 475, "text": "Histone", "colour": "#9999ff", "aliEnd": 521, "start": 465, "href": "http://pfam.xfam.org/family/PF00125.22", "type": "pfama", "display": "true", "metadata": {"end": 522, "description": NaN, "database": "PfamA", "aliStart": 475, "scoreName": "E-value", "accession": "PF00125.22", "start": 465, "score": 0.0029, "identifier": "Core histone H2A/H2B/H3/H4", "type": "DBD", "aliEnd": 521}}], "length": 562}