The Human Transcription Factors

Conclusion

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

Description

Description:	visual system homeobox 2 [Source:HGNC Symbol;Acc:HGNC:1975]
Entrez Summary	TBA
Ensembl ID:	ENSG00000119614
External Link:
Interpro	IPR001356; IPR003654; IPR009057; IPR017970; IPR023339; ;
Protein Domain:
Protein: ENSP00000261980	DBD: Homeodomain	Other: OAR

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:10903837 15647262
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"	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	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Zoo_01		Inferred - vsx2 (98% AA Identity, Danio rerio)
PBM	Barrera2016		Inferred - VSX1 (91% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - VSX1 (91% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Vsx1 (91% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - VSX1 (89% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - ALX4 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (78% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx4 (78% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - ALX4 (78% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - al (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - al (77% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - ALX1 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX1 (77% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx1 (77% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Alx1 (77% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - ALX1 (77% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - ALX1 (77% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (73% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ARX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ARX (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Arx (73% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - UNCX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - UNCX (73% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Uncx (73% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - uncx4.1 (73% AA Identity, Tetraodon nigroviridis)
Transfac	Transfac	License required	Inferred - Arx (73% AA Identity, Rattus norvegicus)
HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX3 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx3 (71% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - ARX (71% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (71% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (71% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (71% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - ARX (71% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - CG2808 (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RAX (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Rax (71% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Rax (71% AA Identity, Rattus norvegicus)
B1H	JASPAR		Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - DMBX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DMBX1 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Dmbx1 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - DRGX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DRGX (68% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - PHDP (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - PHDP (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - PHOX2A (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2A (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2a (68% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2b (68% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Drgx (68% AA Identity, Rattus norvegicus)
Misc	HOMER		Inferred - Phox2a (68% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - VSX1 (67% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
PBM	Barrera2016		Inferred - PHOX2B (66% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PROP1 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Prop1 (66% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - PROP1 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PROP1 (66% AA Identity, Sus scrofa)
Misc	HocoMoco		Inferred - PROP1 (66% AA Identity, Homo sapiens)

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": 205, "endStyle": "curved", "aliStart": 149, "text": "HD", "colour": "#228B22", "aliEnd": 205, "start": 149, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 205, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 149, "scoreName": "E-value", "accession": "PF00046.27", "start": 149, "score": 1.4000000000000002e-23, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 205}}, {"startStyle": "straight", "end": 318, "endStyle": "straight", "aliStart": 300, "text": "OAR", "colour": "#9999ff", "aliEnd": 318, "start": 300, "href": "http://pfam.xfam.org/family/PF03826.15", "type": "pfama", "display": "true", "metadata": {"end": 318, "description": NaN, "database": "PfamA", "aliStart": 300, "scoreName": "E-value", "accession": "PF03826.15", "start": 300, "score": 4.4e-07, "identifier": "OAR domain", "type": "DBD", "aliEnd": 318}}], "length": 362}

TF Info Page for VSX2 (Homeodomain)