The Human Transcription Factors

Conclusion

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

Description

Description:	lysine demethylase 2B [Source:HGNC Symbol;Acc:HGNC:13610]
Entrez Summary	TBA
Ensembl ID:	ENSG00000089094
External Link:
Interpro	IPR001810; IPR001965; IPR002857; IPR003347; IPR006553; IPR011011; IPR019787; ;
Protein Domain:
Protein: ENSP00000366271	DBD: CxxC	Other: Cupin_8, F-box, F-box-like, JmjC, PHD, PHD_4
Protein: ENSP00000445196	DBD: CxxC	Other: Cupin_8, JmjC, PHD_4
Protein: ENSP00000474307	DBD: CxxC	Other:
Protein: ENSP00000366269	DBD: CxxC	Other: Cupin_8, F-box, F-box-like, JmjC, PHD, PHD_4
Protein: ENSP00000437821	DBD: CxxC	Other: F-box, F-box-like, LRR_6, LRR_8, PHD, PHD_4

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	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
PBM	Zoo_01		Direct

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

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Structural comparisons show that the mono-CXXC is homologous  to the structural-zinc binding domain of medium chain  dehydrogenases [4].", "database": "PfamA", "aliStart": 607, "scoreName": "E-value", "accession": "PF02008.18", "start": 605, "score": 1.7e-14, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 651}}, {"startStyle": "straight", "end": 723, "endStyle": "straight", "aliStart": 656, "text": "PHD_4", "colour": "#9999ff", "aliEnd": 722, "start": 656, "href": "http://pfam.xfam.org/family/PF16866.3", "type": "pfama", "display": "true", "metadata": {"end": 723, "description": NaN, "database": "PfamA", "aliStart": 656, "scoreName": "E-value", "accession": "PF16866.3", "start": 656, "score": 3.3e-26, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 722}}, {"startStyle": "straight", "end": 1107, "endStyle": "straight", "aliStart": 1051, "text": "F-box", "colour": "#9999ff", "aliEnd": 1106, "start": 1050, "href": "http://pfam.xfam.org/family/PF00646.31", "type": "pfama", "display": "true", "metadata": {"end": 1107, "description": "This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [3].", "database": "PfamA", "aliStart": 1051, "scoreName": "E-value", "accession": "PF00646.31", "start": 1050, "score": 4e-12, "identifier": "F-box domain", "type": "DBD", "aliEnd": 1106}}, {"startStyle": "jagged", "end": 1108, "endStyle": "straight", "aliStart": 1068, "text": "F-box-like", "colour": "#9999ff", "aliEnd": 1107, "start": 1067, "href": "http://pfam.xfam.org/family/PF12937.5", "type": "pfama", "display": "true", "metadata": {"end": 1108, "description": "This is an F-box-like family.", "database": "PfamA", "aliStart": 1068, "scoreName": "E-value", "accession": "PF12937.5", "start": 1067, "score": 3.4000000000000003e-09, "identifier": "F-box-like", "type": "DBD", "aliEnd": 1107}}, {"startStyle": "jagged", "end": 335, "endStyle": "straight", "aliStart": 142, "text": "Cupin_8", "colour": "#9999ff", "aliEnd": 318, "start": 21, "href": "http://pfam.xfam.org/family/PF13621.4", "type": "pfama", "display": "true", "metadata": {"end": 335, "description": "This cupin like domain shares similarity to the JmjC domain.", "database": "PfamA", "aliStart": 142, "scoreName": "E-value", "accession": "PF13621.4", "start": 21, "score": 3.3e-07, "identifier": "Cupin-like domain", "type": "DBD", "aliEnd": 318}}, {"startStyle": "straight", "end": 329, "endStyle": "straight", "aliStart": 229, "text": "JmjC", "colour": "#9999ff", "aliEnd": 322, "start": 229, "href": "http://pfam.xfam.org/family/PF02373.20", "type": "pfama", "display": "true", "metadata": {"end": 329, "description": "The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].", "database": "PfamA", "aliStart": 229, "scoreName": "E-value", "accession": "PF02373.20", "start": 229, "score": 2.4e-06, "identifier": "JmjC domain, hydroxylase", "type": "DBD", "aliEnd": 322}}, {"startStyle": "straight", "end": 725, "endStyle": "straight", "aliStart": 662, "text": "PHD", "colour": "#9999ff", "aliEnd": 724, "start": 661, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 725, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 662, "scoreName": "E-value", "accession": "PF00628.27", "start": 661, "score": 0.0025, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 724}}], "length": 1337}

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JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].", "database": "PfamA", "aliStart": 198, "scoreName": "E-value", "accession": "PF02373.20", "start": 198, "score": 5.3e-06, "identifier": "JmjC domain, hydroxylase", "type": "DBD", "aliEnd": 291}}, {"startStyle": "straight", "end": 694, "endStyle": "straight", "aliStart": 631, "text": "PHD", "colour": "#9999ff", "aliEnd": 693, "start": 630, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 694, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  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TF Info Page for KDM2B (CxxC)