TF Info Page for NKX2-3 (Homeodomain)

Conclusion

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

Description

Description: NK2 homeobox 3 [Source:HGNC Symbol;Acc:HGNC:7836]
Entrez Summary This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]
Ensembl ID: ENSG00000119919
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000342828
Protein Domain: ENSP00000479692
Domain:
Protein: ENSP00000342828DBD: HomeodomainOther:
Protein: ENSP00000479692DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_DNA-Binding
sequence-specific_Transactivation_
PMIDS:10790368 12141427
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
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Nkx2-3 (100% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (92% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-5 (92% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-5 (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (92% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Nkx2-5 (92% AA Identity, Mus musculus)
SELEXJASPARInferred - Nkx2-5 (92% AA Identity, Mus musculus)
MiscHocoMocoInferred - NKX2-5 (92% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-5 (92% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (91% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - NKX2-5 (91% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-6 (85% AA Identity, Mus musculus)
HT-SELEXNitta2015Inferred - scro (85% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Nkx2-1 (84% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx2-4 (84% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-1 (84% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (84% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (84% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (84% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX2-1 (84% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-1 (84% AA Identity, Mus musculus)
PBMZoo_01Inferred - ceh-24 (80% AA Identity, Caenorhabditis elegans)
PBMBerger08Inferred - Nkx2-2 (80% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-2 (80% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-2 (80% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-2 (80% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX2-2 (80% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - NKX2-8 (78% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-8 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-8 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-8 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-8 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-9 (78% AA Identity, Mus musculus)
PBMDREAM_contestInferred - Nkx2-9 (78% AA Identity, Mus musculus)
B1HJASPARInferred - vnd (78% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - NKX2-8 (78% AA Identity, Homo sapiens)
MisciDMMPMMInferred - vnd (78% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - NKX2-8 (77% AA Identity, Homo sapiens)
ChIP-seqmodENCODEInferred - ceh-28 (77% AA Identity, Caenorhabditis elegans)
HT-SELEXYin2017Inferred - NKX3-2 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx3-2 (75% AA Identity, Mus musculus)
SELEXJASPARInferred - NKX3-2 (75% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX3-2 (75% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX3-2 (75% AA Identity, Homo sapiens)
PBMBusserDevelopment2012Inferred - bap (73% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - bap (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - bap (73% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - bap (73% AA Identity, Drosophila melanogaster)
PBMBerger06Inferred - ceh-22 (70% AA Identity, Caenorhabditis elegans)
PBMJASPARInferred - ceh-22 (70% AA Identity, Caenorhabditis elegans)
HT-SELEXYin2017Inferred - NKX3-1 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-1 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-1 (70% AA Identity, Homo sapiens)
PBMBadis09Inferred - Nkx3-1 (70% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx3-1 (70% AA Identity, Mus musculus)
PBMBusserDevelopment2012Inferred - tin (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - tin (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - NKX3-1 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX3-1 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX3-1 (70% AA Identity, Homo sapiens)
SELEXJASPARInferred - Nkx3-1 (70% AA Identity, Mus musculus)
ChIP-chipJASPARInferred - tin (70% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - NKX3-1 (70% AA Identity, Homo sapiens)
MiscHOMERInferred - NKX3-1 (70% 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