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

Gene ID: 4824, updated on 4-Jan-2025

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; AllianceGenome:HGNC:7838
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
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (23678693..23682938, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23953650..23957884, complement)
RS_2024_09 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 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23507883-23508510 Neighboring gene uncharacterized LOC107986930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23561989-23562888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23566930-23567494 Neighboring gene uncharacterized LOC101929258 Neighboring gene NK2 homeobox 6

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific  
enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific  
enables DNA-binding transcription factor binding PubMed 
enables MADS box domain binding  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
enables cysteine-type endopeptidase activator activity involved in apoptotic process PubMed 
enables histone deacetylase binding PubMed 
enables nuclear estrogen receptor binding PubMed 
enables nuclear receptor activity PubMed 
enables protein binding PubMed 
enables sequence-specific DNA binding PubMed 
enables sequence-specific double-stranded DNA binding PubMed 
enables transcription cis-regulatory region binding PubMed 
enables transcription regulator inhibitor activity PubMed 
Items 1 - 25 of 46
Process Evidence Code Pubs
involved_in DNA damage response PubMed 
involved_in androgen receptor signaling pathway PubMed 
involved_in apoptotic process  
involved_in branching involved in prostate gland morphogenesis  
involved_in branching morphogenesis of an epithelial tube  
involved_in cell differentiation  
involved_in cellular response to hypoxia PubMed 
involved_in cellular response to interleukin-1 PubMed 
involved_in cellular response to steroid hormone stimulus PubMed 
involved_in cellular response to tumor necrosis factor PubMed 
involved_in cellular response to xenobiotic stimulus PubMed 
involved_in dorsal aorta development  
involved_in epithelial cell proliferation involved in prostate gland development  
involved_in epithelial cell proliferation involved in salivary gland morphogenesis  
involved_in heart development  
involved_in male gonad development  
involved_in metanephros development  
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of cell population proliferation PubMed 
involved_in negative regulation of epithelial cell proliferation  
involved_in negative regulation of epithelial cell proliferation involved in prostate gland development  
involved_in negative regulation of gene expression PubMed 
involved_in negative regulation of insulin-like growth factor receptor signaling pathway  
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in pharyngeal system development  
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription  
involved_in positive regulation of androgen secretion PubMed 
involved_in positive regulation of apoptotic signaling pathway PubMed 
involved_in positive regulation of cell division PubMed 
involved_in positive regulation of cell population proliferation PubMed 
involved_in positive regulation of cysteine-type endopeptidase activity PubMed 
involved_in positive regulation of gene expression PubMed 
involved_in positive regulation of gene expression PubMed 
involved_in positive regulation of intrinsic apoptotic signaling pathway PubMed 
involved_in positive regulation of mitotic cell cycle PubMed 
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction PubMed 
involved_in positive regulation of protein phosphorylation PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in regulation of DNA-templated transcription PubMed 
involved_in regulation of protein localization PubMed 
involved_in regulation of transcription by RNA polymerase II  
involved_in response to testosterone  
involved_in salivary gland development  
involved_in somitogenesis  
Items 1 - 25 of 46
Component Evidence Code Pubs
located_in chromatin  
located_in cytosol  
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 
located_in nucleus PubMed 
located_in nucleus PubMed 
located_in site of DNA damage 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
    O15465, Q99801, Q9H2P4, Q9H2P5, Q9H2P6, Q9H2P7, Q9HBG0
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    23953650..23957884 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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