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

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: mouse all
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Genomic context

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NKX3.1 Expression in Non-Prostatic Tumors and Characterizing its Expression in Esophageal/Gastroesophageal Adenocarcinoma.
Title: NKX3.1 Expression in Non-Prostatic Tumors and Characterizing its Expression in Esophageal/Gastroesophageal Adenocarcinoma.
Comprehensive Analysis of NKX3.2 in Liver Hepatocellular Carcinoma by Bigdata.
Title: Comprehensive Analysis of NKX3.2 in Liver Hepatocellular Carcinoma by Bigdata.
Fibroblast-derived exosomal microRNA regulates NKX3-1 expression in androgen-sensitive, androgen receptor-dependent prostate cancer cells.
Title: Fibroblast-derived exosomal microRNA regulates NKX3-1 expression in androgen-sensitive, androgen receptor-dependent prostate cancer cells.
NKX3.1 Expression and Molecular Characterization of Secretory Myoepithelial Carcinoma (SMCA): Advancing the Case for a Salivary Mucous Acinar Phenotype.
Title: NKX3.1 Expression and Molecular Characterization of Secretory Myoepithelial Carcinoma (SMCA): Advancing the Case for a Salivary Mucous Acinar Phenotype.
Genome-Wide 3'-UTR Single Nucleotide Polymorphism Association Study Identifies Significant Prostate Cancer Risk-Associated Functional Loci at 8p21.2 in Chinese Population.
Title: Genome-Wide 3'-UTR Single Nucleotide Polymorphism Association Study Identifies Significant Prostate Cancer Risk-Associated Functional Loci at 8p21.2 in Chinese Population.
Gene of the month: NKX3.1.
Title: Gene of the month: NKX3.1.
NKX3.1 immunohistochemistry is highly specific for the diagnosis of mesenchymal chondrosarcomas: experience in the Australian population.
Title: NKX3.1 immunohistochemistry is highly specific for the diagnosis of mesenchymal chondrosarcomas: experience in the Australian population.
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness.
Title: Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness.
NKX3.1 a useful marker for mesenchymal chondrosarcoma: An immunohistochemical study.
Title: NKX3.1 a useful marker for mesenchymal chondrosarcoma: An immunohistochemical study.
Differential expression of NKX 3.1 and HOXB 13 in bone metastases originating from prostatic carcinoma among the Egyptian males.
Title: Differential expression of NKX 3.1 and HOXB 13 in bone metastases originating from prostatic carcinoma among the Egyptian males.

Submit: New GeneRIF Correction See all GeneRIFs (96)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:482056

RH94244 (e-PCR)
- UniSTS:83723

NKX3-1_1192 (e-PCR)
- UniSTS:277532

NoName (e-PCR)
- UniSTS:481847

NoName (e-PCR)
- UniSTS:486723

SHGC-57295 (e-PCR)
- UniSTS:75189

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

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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)

NM_001256339.1 → NP_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:52 → 105

Homeobox; Homeobox domain
NM_006167.4 → NP_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:127 → 180

Homeobox; Homeobox domain

RNA

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