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

    Gene ID: 4824, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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: 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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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
     
    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 histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables nuclear estrogen receptor binding IDA
    Inferred from Direct Assay
    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 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 DNA damage response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in androgen receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    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 cellular response to xenobiotic stimulus 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 prostate gland 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 negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    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 transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in pharyngeal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    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 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 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/protein kinase B signal transduction 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 transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    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
     
    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
     
    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)

    NEW Try the new Transcript table

    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)