TF Info Page for NKX3-1 (Homeodomain)

Conclusion

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

Description

Description: NK3 homeobox 1 [Source:HGNC Symbol;Acc:HGNC:7838]
Entrez Summary This gene encodes a homeobox-containing transcription factor. This transcription factor functions as a negative regulator of epithelial cell growth in prostate tissue. Aberrant expression of this gene is associated with prostate tumor progression. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jan 2012]
Ensembl ID: ENSG00000167034
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000370253
Protein Domain: ENSP00000429729
Domain:
Protein: ENSP00000370253DBD: HomeodomainOther:
Protein: ENSP00000429729DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:10993896
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:0000983
RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity
IEA - GO_REF:0000019
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:20855495 | NAS - PMID:11137288
GO:0004882
androgen receptor activity
IDA - PMID:19886863
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
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHOMERDirect
PBMBadis09Inferred - Nkx3-1 (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx3-1 (100% AA Identity, Mus musculus)
SELEXJASPARInferred - Nkx3-1 (100% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - NKX3-2 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (84% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx3-2 (84% AA Identity, Mus musculus)
SELEXJASPARInferred - NKX3-2 (84% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX3-2 (84% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX3-2 (84% AA Identity, Homo sapiens)
PBMBusserDevelopment2012Inferred - bap (78% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - bap (78% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - bap (78% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - bap (78% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-3 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-5 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-5 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-5 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (68% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Nkx2-5 (68% AA Identity, Mus musculus)
SELEXJASPARInferred - Nkx2-5 (68% AA Identity, Mus musculus)
MiscHocoMocoInferred - NKX2-5 (68% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-5 (68% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx2-1 (66% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx2-4 (66% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - NKX2-5 (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - NKX2-8 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX2-1 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-1 (66% 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