The Human Transcription Factors

Conclusion

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

Description

Description:	runt related transcription factor 2 [Source:HGNC Symbol;Acc:HGNC:10472]
Entrez Summary	TBA
Ensembl ID:	ENSG00000124813
External Link:	T139288_1.02
Interpro	IPR000040; IPR008967; IPR013524; IPR013711; IPR016554; ;
Protein Domain:
Protein: ENSP00000485863	DBD: RUNX	Other: DUF2722, RunxI, Spt20
Protein: ENSP00000352514	DBD: RUNX	Other: DUF2722, RunxI, Spt20

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:11451945 16574347
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:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity IBA - GO_REF:0000033 GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:9182765
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	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
Misc	HOMER		Direct
PBM	TF_Evolution	Unpublished Data	Inferred - Runx2 (100% AA Identity, Mus musculus)
HT-SELEX	Jolma2010		Inferred - RUNX3 (94% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - RUNX3 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RUNX1 (92% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Runx1 (92% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - RUNX1 (92% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Runx1 (92% AA Identity, Mus musculus)

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": 217, "endStyle": "curved", "aliStart": 89, "text": "Runt", "colour": "#228B22", "aliEnd": 216, "start": 88, "href": "http://pfam.xfam.org/family/PF00853.17", "type": "pfama", "display": "true", "metadata": {"end": 217, "description": "The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia [PUBMED:7651838]. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene [PUBMED:7651838]. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction.", "database": "PfamA", "aliStart": 89, "scoreName": "E-value", "accession": "PF00853.17", "start": 88, "score": 8.3e-74, "identifier": "Runt domain", "type": "DBD", "aliEnd": 216}}, {"startStyle": "straight", "end": 485, "endStyle": "straight", "aliStart": 395, "text": "RunxI", "colour": "#9999ff", "aliEnd": 485, "start": 394, "href": "http://pfam.xfam.org/family/PF08504.9", "type": "pfama", "display": "true", "metadata": {"end": 485, "description": "This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2).  Its function might be to interact with functional cofactors [1].", "database": "PfamA", "aliStart": 395, "scoreName": "E-value", "accession": "PF08504.9", "start": 394, "score": 2.4e-40, "identifier": "Runx inhibition domain", "type": "DBD", "aliEnd": 485}}, {"startStyle": "straight", "end": 292, "endStyle": "jagged", "aliStart": 26, "text": "DUF2722", "colour": "#9999ff", "aliEnd": 67, "start": 18, "href": "http://pfam.xfam.org/family/PF10846.6", "type": "pfama", "display": "true", "metadata": {"end": 292, "description": "This eukaryotic family of proteins has no known function.", "database": "PfamA", "aliStart": 26, "scoreName": "E-value", "accession": "PF10846.6", "start": 18, "score": 4.2999999999999995e-06, "identifier": "Protein of unknown function (DUF2722)", "type": "DBD", "aliEnd": 67}}, {"startStyle": "jagged", "end": 90, "endStyle": "jagged", "aliStart": 30, "text": "Spt20", "colour": "#9999ff", "aliEnd": 62, "start": 9, "href": "http://pfam.xfam.org/family/PF12090.6", "type": "pfama", "display": "true", "metadata": {"end": 90, "description": "This presumed domain is found in the Spt20 proteins from both human and yeast.  The Spt20 protein is part of the SAGA complex which is a large complex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.", "database": "PfamA", "aliStart": 30, "scoreName": "E-value", "accession": "PF12090.6", "start": 9, "score": 0.0057, "identifier": "Spt20 family", "type": "DBD", "aliEnd": 62}}], "length": 486}

{"regions": [{"startStyle": "curved", "end": 217, "endStyle": "curved", "aliStart": 89, "text": "Runt", "colour": "#228B22", "aliEnd": 216, "start": 88, "href": "http://pfam.xfam.org/family/PF00853.17", "type": "pfama", "display": "true", "metadata": {"end": 217, "description": "The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia [PUBMED:7651838]. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene [PUBMED:7651838]. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction.", "database": "PfamA", "aliStart": 89, "scoreName": "E-value", "accession": "PF00853.17", "start": 88, "score": 8.999999999999998e-74, "identifier": "Runt domain", "type": "DBD", "aliEnd": 216}}, {"startStyle": "straight", "end": 507, "endStyle": "straight", "aliStart": 417, "text": "RunxI", "colour": "#9999ff", "aliEnd": 507, "start": 416, "href": "http://pfam.xfam.org/family/PF08504.9", "type": "pfama", "display": "true", "metadata": {"end": 507, "description": "This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2).  Its function might be to interact with functional cofactors [1].", "database": "PfamA", "aliStart": 417, "scoreName": "E-value", "accession": "PF08504.9", "start": 416, "score": 2.5e-40, "identifier": "Runx inhibition domain", "type": "DBD", "aliEnd": 507}}, {"startStyle": "straight", "end": 289, "endStyle": "jagged", "aliStart": 26, "text": "DUF2722", "colour": "#9999ff", "aliEnd": 67, "start": 18, "href": "http://pfam.xfam.org/family/PF10846.6", "type": "pfama", "display": "true", "metadata": {"end": 289, "description": "This eukaryotic family of proteins has no known function.", "database": "PfamA", "aliStart": 26, "scoreName": "E-value", "accession": "PF10846.6", "start": 18, "score": 4.8e-06, "identifier": "Protein of unknown function (DUF2722)", "type": "DBD", "aliEnd": 67}}, {"startStyle": "jagged", "end": 90, "endStyle": "jagged", "aliStart": 30, "text": "Spt20", "colour": "#9999ff", "aliEnd": 62, "start": 9, "href": "http://pfam.xfam.org/family/PF12090.6", "type": "pfama", "display": "true", "metadata": {"end": 90, "description": "This presumed domain is found in the Spt20 proteins from both human and yeast.  The Spt20 protein is part of the SAGA complex which is a large complex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.", "database": "PfamA", "aliStart": 30, "scoreName": "E-value", "accession": "PF12090.6", "start": 9, "score": 0.006, "identifier": "Spt20 family", "type": "DBD", "aliEnd": 62}}], "length": 508}

TF Info Page for RUNX2 (Runt)