The Human Transcription Factors

Conclusion

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

Description

Description:	short stature homeobox [Source:HGNC Symbol;Acc:HGNC:10853]
Entrez Summary	TBA
Ensembl ID:	ENSG00000185960
External Link:	T093403_1.02
Interpro	IPR000047; IPR001356; IPR003654; IPR009057; IPR017970; ;
Protein Domain:
Protein: ENSP00000370987	DBD: Homeodomain	Other:
Protein: ENSP00000452016	DBD: Homeodomain	Other: OAR
Protein: ENSP00000335505	DBD: Homeodomain	Other:
Protein: ENSP00000370990	DBD: Homeodomain	Other: OAR

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.	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 TAS - PMID:9259282
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
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
PBM	Zoo_01		Direct
PBM	Berger08		Inferred - Shox2 (100% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Shox2 (100% AA Identity, Rattus norvegicus)
HT-SELEX	Nitta2015		Inferred - CG5369 (96% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG5369 (96% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG5369 (96% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - SNAPOd2T00006620001 (84% AA Identity, Oikopleura dioica)
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)
Transfac	Transfac	License required	Inferred - Arx (73% AA Identity, Rattus norvegicus)
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)
B1H	JASPAR		Inferred - CG11294 (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG11294 (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG11294 (71% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - hbn (71% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - hbn (71% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Otp (71% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - UNCX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - UNCX (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Uncx (71% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - uncx4.1 (71% AA Identity, Tetraodon nigroviridis)
B1H	JASPAR		Inferred - otp (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - otp (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - otp (70% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - PHDP (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - PHDP (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - PHOX2A (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2A (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2a (70% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PHOX2B (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PHOX2B (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PHOX2B (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Phox2b (70% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - Pph13 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Pph13 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Prrx2 (70% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - unc-4 (70% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - unc-4 (70% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - PRRX2 (70% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - Prrx2 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Prrx2 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - PRRX2 (70% AA Identity, Sus scrofa)
Misc	HOMER		Inferred - Phox2a (70% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - PRRX2 (70% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - al (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - al (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG2808 (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - DRGX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - DRGX (68% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - NEMVEDRAFT_v1g105595 (68% AA Identity, Nematostella vectensis)
PBM	Barrera2016		Inferred - PHOX2B (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Drgx (68% AA Identity, Rattus norvegicus)
HT-SELEX	Yin2017		Inferred - ALX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX1 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx1 (66% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Alx1 (66% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - ALX4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ALX4 (66% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Alx4 (66% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - CG9876 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (66% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG9876 (66% AA Identity, Drosophila melanogaster)
PBM	Berger08		Inferred - Prrx1 (66% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - si:dkey-43p13.5 (66% AA Identity, Danio rerio)
Transfac	Transfac	License required	Inferred - ALX1 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - ALX4 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PRRX1 (66% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Prrx1 (66% AA Identity, Rattus norvegicus)
Misc	HocoMoco		Inferred - ALX1 (66% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - PRRX1 (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": 174, "endStyle": "curved", "aliStart": 118, "text": "HD", "colour": "#228B22", "aliEnd": 174, "start": 118, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 174, "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": 118, "scoreName": "E-value", "accession": "PF00046.27", "start": 118, "score": 7.1e-25, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 174}}, {"startStyle": "jagged", "end": 288, "endStyle": "straight", "aliStart": 272, "text": "OAR", "colour": "#9999ff", "aliEnd": 288, "start": 271, "href": "http://pfam.xfam.org/family/PF03826.15", "type": "pfama", "display": "true", "metadata": {"end": 288, "description": NaN, "database": "PfamA", "aliStart": 272, "scoreName": "E-value", "accession": "PF03826.15", "start": 271, "score": 2e-07, "identifier": "OAR domain", "type": "DBD", "aliEnd": 288}}], "length": 293}

TF Info Page for SHOX (Homeodomain)