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

Gene ID: 4824, updated on 22-Aug-2021

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
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Genomic context

See NKX3-1 in Genome Data Viewer
Location:
8p21.2
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (23678693..23682938, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (23536206..23540451, 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
GeneReviews: Not available
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
GeneReviews: Not available
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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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_046072.2 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)
    AC012574, AC051642, BC111574, BF511129

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    23678693..23682938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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