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NKX3-1 NK3 homeobox 1 [ Homo sapiens (human) ]

Gene ID: 4824, updated on 15-Apr-2019

Summary

Official Symbol
NKX3-1provided by HGNC
Official Full Name
NK3 homeobox 1provided by HGNC
Primary source
HGNC:HGNC:7838
See related
Ensembl:ENSG00000167034 MIM:602041
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NKX3; BAPX2; NKX3A; NKX3.1
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]
Expression
Biased expression in prostate (RPKM 180.9) and testis (RPKM 17.6) See more
Orthologs

Genomic context

See NKX3-1 in Genome Data Viewer
Location:
8p21.2
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (23678693..23682937, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (23536206..23540450, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene RNA, U4 small nuclear 71, pseudogene Neighboring gene SINHCAF pseudogene 3 Neighboring gene uncharacterized LOC107986930 Neighboring gene uncharacterized LOC101929258 Neighboring gene NK2 homeobox 6

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
NHGRI GWA Catalog
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
NHGRI GWA Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
MADS box domain binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
cysteine-type endopeptidase activator activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
estrogen receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein self-association IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
androgen receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
branching involved in prostate gland morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
branching morphogenesis of an epithelial tube ISS
Inferred from Sequence or Structural Similarity
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to drug IEP
Inferred from Expression Pattern
more info
PubMed 
cellular response to hypoxia IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to interleukin-1 IEP
Inferred from Expression Pattern
more info
PubMed 
cellular response to steroid hormone stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
PubMed 
dorsal aorta development IEA
Inferred from Electronic Annotation
more info
 
epithelial cell proliferation involved in salivary gland morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
metanephros development IEA
Inferred from Electronic Annotation
more info
 
mitotic cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of epithelial cell proliferation involved in prostate gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of estrogen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of insulin-like growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
pharyngeal system development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of androgen secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell death IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell division IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of intrinsic apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of phosphatidylinositol 3-kinase signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
protein kinase B signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
response to testosterone ISS
Inferred from Sequence or Structural Similarity
more info
 
salivary gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
somitogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
site of DNA damage IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
homeobox protein Nkx-3.1
Names
NK homeobox, family 3, A
NK3 transcription factor homolog A
NK3 transcription factor related, locus 1
homeobox protein NK-3 homolog A

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001256339.1NP_001243268.1  homeobox protein Nkx-3.1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC051642, AF249672, BF511129
    Consensus CDS
    CCDS59095.1
    UniProtKB/Swiss-Prot
    Q99801
    Related
    ENSP00000429729.1, ENST00000523261.1
    Conserved Domains (1) summary
    pfam00046
    Location:52105
    Homeobox; Homeobox domain
  2. NM_006167.4NP_006158.2  homeobox protein Nkx-3.1 isoform 1

    See identical proteins and their annotated locations for NP_006158.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC012574, AC051642, AF247704
    Consensus CDS
    CCDS6042.1
    UniProtKB/Swiss-Prot
    Q99801
    Related
    ENSP00000370253.4, ENST00000380871.5
    Conserved Domains (1) summary
    pfam00046
    Location:127180
    Homeobox; Homeobox domain

RNA

  1. NR_046072.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC051642, BC111574, BF511129

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    23678693..23682937 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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