The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Inferred motif	1 Monomer or homomultimer	High-throughput in vitro		In the structure (PDB: 5FD3), the protein contacts DNA, although it only contacts the backbone except for one tyrosine residue

Description

Description:	lin-54 DREAM MuvB core complex component [Source:HGNC Symbol;Acc:HGNC:25397]
Entrez Summary	TBA
Ensembl ID:	ENSG00000189308
External Link:
Interpro	IPR005172; ;
Protein Domain:
Protein: ENSP00000341947	DBD: CxC	Other:
Protein: ENSP00000398265	DBD: CxC	Other:
Protein: ENSP00000407139	DBD: CxC	Other:
Protein: ENSP00000423475	DBD: CxC	Other:
Protein: ENSP00000421045	DBD: CxC	Other:

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.	No
CisBP considers it as a TF?	Yes
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	3a, decent circumstantial evidence for its role as
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
PBM	Zoo_01		Inferred - LIN54 (98% AA Identity, Gallus gallus)
PBM	Zoo_01		Inferred - LIN54 (94% AA Identity, Tarsius syrichta)
PBM	Zoo_01		Inferred - lin54 (92% AA Identity, Danio rerio)
PBM	Zoo_01		Inferred - SPU_025306 (88% AA Identity, Strongylocentrotus purpuratus)
PBM	TF_Evolution	Unpublished Data	Inferred - NEMVEDRAFT_v1g111410 (84% AA Identity, Nematostella vectensis)
PBM	TF_Evolution	Unpublished Data	Inferred - XP_002124866.1 (82% AA Identity, Ciona intestinalis)
PBM	Zoo_01		Inferred - BGIBMGA008956 (81% AA Identity, Bombyx mori)
PBM	Zoo_01		Inferred - GE12548 (80% AA Identity, Drosophila yakuba)

Structure

Structure	PDB	5FD3

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": "curved", "end": 469, "endStyle": "curved", "aliStart": 434, "text": "TCR", "colour": "#2cb42c", "aliEnd": 468, "start": 433, "href": "http://pfam.xfam.org/family/PF03638.13", "type": "pfama", "display": "true", "metadata": {"end": 469, "description": "This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin Swiss:Q9Y4I5 [1] and TSO1 Swiss:Q9LE32 [2]. This family is called a CXC domain in [2].", "database": "PfamA", "aliStart": 434, "scoreName": "E-value", "accession": "PF03638.13", "start": 433, "score": 1.2e-22, "identifier": "Tesmin/TSO1-like CXC domain, cysteine-rich domain", "type": "DBD", "aliEnd": 468}}, {"startStyle": "curved", "end": 544, "endStyle": "curved", "aliStart": 508, "text": "TCR", "colour": "#2cb42c", "aliEnd": 543, "start": 507, "href": "http://pfam.xfam.org/family/PF03638.13", "type": "pfama", "display": "true", "metadata": {"end": 544, "description": "This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin Swiss:Q9Y4I5 [1] and TSO1 Swiss:Q9LE32 [2]. This family is called a CXC domain in [2].", "database": "PfamA", "aliStart": 508, "scoreName": "E-value", "accession": "PF03638.13", "start": 507, "score": 1.2e-22, "identifier": "Tesmin/TSO1-like CXC domain, cysteine-rich domain", "type": "DBD", "aliEnd": 543}}], "length": 661}

TF Info Page for LIN54 (TCR/CxC)