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] See more...

Aliases for NKX3-1 Gene

Aliases for NKX3-1 Gene

  • NK3 Homeobox 1 2 3 5
  • NKX3.1 2 3 4
  • Homeobox Protein NK-3 Homolog A 3 4
  • Homeobox Protein Nkx-3.1 3 4
  • BAPX2 2 3
  • NKX3A 3 4
  • NK3 Transcription Factor Related, Locus 1 (Drosophila) 2
  • NK3 Transcription Factor Related, Locus 1 3
  • NK Homeobox (Drosophila), Family 3, A 2
  • NK3 Transcription Factor Homolog A 3
  • NK Homeobox, Family 3, A 3
  • NKX3-1 5
  • NKX3 3

External Ids for NKX3-1 Gene

Previous HGNC Symbols for NKX3-1 Gene

  • NKX3A

Previous GeneCards Identifiers for NKX3-1 Gene

  • GC08M023268
  • GC08M023889
  • GC08M023558
  • GC08M023592
  • GC08M022081
  • GC08M023536

Summaries for NKX3-1 Gene

Entrez Gene Summary for NKX3-1 Gene

  • 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]

GeneCards Summary for NKX3-1 Gene

NKX3-1 (NK3 Homeobox 1) is a Protein Coding gene. Diseases associated with NKX3-1 include Prostatitis and Chromosome 8P Deletion. Among its related pathways are Coregulation of Androgen receptor activity and FOXA1 transcription factor network. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription factor binding. An important paralog of this gene is NKX3-2.

UniProtKB/Swiss-Prot Summary for NKX3-1 Gene

  • Transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and can behave as a transcriptional repressor. Plays an important role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. Acts as a tumor suppressor controlling prostate carcinogenesis, as shown by the ability to inhibit proliferation and invasion activities of PC-3 prostate cancer cells.

Gene Wiki entry for NKX3-1 Gene

Additional gene information for NKX3-1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NKX3-1 Gene

Genomics for NKX3-1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NKX3-1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NKX3-1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NKX3-1

Top Transcription factor binding sites by QIAGEN in the NKX3-1 gene promoter:
  • C/EBPalpha
  • FOXO1
  • FOXO1a
  • HTF
  • p53
  • PPAR-gamma1
  • PPAR-gamma2
  • SRF
  • SRF (504 AA)

Genomic Locations for NKX3-1 Gene

Genomic Locations for NKX3-1 Gene
chr8:23,678,693-23,682,938
(GRCh38/hg38)
Size:
4,246 bases
Orientation:
Minus strand
chr8:23,536,206-23,540,450
(GRCh37/hg19)
Size:
4,245 bases
Orientation:
Minus strand

Genomic View for NKX3-1 Gene

Genes around NKX3-1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX3-1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX3-1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX3-1 Gene

Proteins for NKX3-1 Gene

  • Protein details for NKX3-1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99801-NKX31_HUMAN
    Recommended name:
    Homeobox protein Nkx-3.1
    Protein Accession:
    Q99801
    Secondary Accessions:
    • O15465
    • Q9H2P4
    • Q9H2P5
    • Q9H2P6
    • Q9H2P7
    • Q9HBG0

    Protein attributes for NKX3-1 Gene

    Size:
    234 amino acids
    Molecular mass:
    26350 Da
    Quaternary structure:
    • Interacts with serum response factor (SRF) (By similarity). Interacts with SPDEF. Interacts with WDR77. Interacts with TOPORS which polyubiquitinates NKX3-1 and induces its proteasomal degradation.

    Three dimensional structures from OCA and Proteopedia for NKX3-1 Gene

    Alternative splice isoforms for NKX3-1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NKX3-1 Gene

Post-translational modifications for NKX3-1 Gene

  • Ubiquitinated by TOPORS; monoubiquitinated at several residues and also polyubiquitinated on single residues.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX3-1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for NKX3-1

No data available for DME Specific Peptides for NKX3-1 Gene

Domains & Families for NKX3-1 Gene

Gene Families for NKX3-1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for NKX3-1 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
ProtoNet:

Suggested Antigen Peptide Sequences for NKX3-1 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein NK-3 homolog A (NKX31_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q99801

UniProtKB/Swiss-Prot:

NKX31_HUMAN :
  • Belongs to the NK-3 homeobox family.
Family:
  • Belongs to the NK-3 homeobox family.
genes like me logo Genes that share domains with NKX3-1: view

Function for NKX3-1 Gene

Molecular function for NKX3-1 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and can behave as a transcriptional repressor. Plays an important role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. Acts as a tumor suppressor controlling prostate carcinogenesis, as shown by the ability to inhibit proliferation and invasion activities of PC-3 prostate cancer cells.
UniProtKB/Swiss-Prot Induction:
By androgens and, in the LNCaP cell line, by estrogens. Androgenic control may be lost in prostate cancer cells during tumor progression from an androgen-dependent to an androgen-independent phase.

Phenotypes From GWAS Catalog for NKX3-1 Gene

Gene Ontology (GO) - Molecular Function for NKX3-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 19263243
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 18974119
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IDA,NAS 11137288
genes like me logo Genes that share ontologies with NKX3-1: view
genes like me logo Genes that share phenotypes with NKX3-1: view

Animal Models for NKX3-1 Gene

MGI Knock Outs for NKX3-1:

Animal Model Products

CRISPR Products

miRNA for NKX3-1 Gene

Transcription Factor Targets for NKX3-1 Gene

Selected GeneGlobe predicted Target genes for NKX3-1
Targeted motifs for NKX3-1 Gene
HOMER Transcription Factor Regulatory Elements motif NKX3-1
  • Consensus sequence: AAGCACTTAA Submotif: canonical Cell Type: LNCaP GEO ID: GSE28264

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX3-1

No data available for Enzyme Numbers (IUBMB) and Human Phenotype Ontology for NKX3-1 Gene

Localization for NKX3-1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX3-1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NKX3-1 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NKX3-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA,NAS 11137288
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0090734 site of DNA damage IDA 20395202
genes like me logo Genes that share ontologies with NKX3-1: view

Pathways & Interactions for NKX3-1 Gene

genes like me logo Genes that share pathways with NKX3-1: view

SIGNOR curated interactions for NKX3-1 Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for NKX3-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001655 urogenital system development IEA --
GO:0001656 metanephros development IEA --
GO:0001756 somitogenesis IEA --
GO:0001934 positive regulation of protein phosphorylation IDA 20395202
GO:0006355 regulation of transcription, DNA-templated NAS 11137288
genes like me logo Genes that share ontologies with NKX3-1: view

Drugs & Compounds for NKX3-1 Gene

(2) Drugs for NKX3-1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for NKX3-1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NKX3-1: view

Transcripts for NKX3-1 Gene

mRNA/cDNA for NKX3-1 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX3-1

Alternative Splicing Database (ASD) splice patterns (SP) for NKX3-1 Gene

No ASD Table

Relevant External Links for NKX3-1 Gene

GeneLoc Exon Structure for
NKX3-1

Expression for NKX3-1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NKX3-1 Gene

mRNA differential expression in normal tissues according to GTEx for NKX3-1 Gene

This gene is overexpressed in Prostate (x29.4) and Minor Salivary Gland (x7.0).

Protein differential expression in normal tissues from HIPED for NKX3-1 Gene

This gene is overexpressed in Heart (43.8) and Prostate (24.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NKX3-1 Gene



Protein tissue co-expression partners for NKX3-1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NKX3-1

SOURCE GeneReport for Unigene cluster for NKX3-1 Gene:

Hs.55999

mRNA Expression by UniProt/SwissProt for NKX3-1 Gene:

Q99801-NKX31_HUMAN
Tissue specificity: Highly expressed in the prostate and, at a lower level, in the testis.

Evidence on tissue expression from TISSUES for NKX3-1 Gene

  • Lung(4.3)
  • Nervous system(2.4)
  • Intestine(2.2)
  • Skin(2.2)
  • Muscle(2.2)
  • Liver(2.1)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with NKX3-1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX3-1 Gene

Orthologs for NKX3-1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NKX3-1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NKX3-1 30 31
  • 99.3 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NKX3-1 30 31
  • 87.86 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NKX3-1 30 31
  • 80.48 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Nkx3-1 30 17 31
  • 73.6 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Nkx3-1 30
  • 72.15 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia NKX3-1 31
  • 66 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NKX3-1 31
  • 59 (a)
OneToOne
Chicken
(Gallus gallus)
Aves NKX3-1 30
  • 60.93 (n)
SOHO-1 31
  • 21 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia NKX3-1 31
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nkx3-1 30
  • 56.68 (n)
Str.5202 30
African clawed frog
(Xenopus laevis)
Amphibia nkx3-1-prov 30
Zebrafish
(Danio rerio)
Actinopterygii nkx3-1 30 31
  • 65.15 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta bap 31
  • 21 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ceh-27 31
  • 19 (a)
ManyToMany
Species where no ortholog for NKX3-1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for NKX3-1 Gene

ENSEMBL:
Gene Tree for NKX3-1 (if available)
TreeFam:
Gene Tree for NKX3-1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKX3-1: view image

Paralogs for NKX3-1 Gene

(1) SIMAP similar genes for NKX3-1 Gene using alignment to 1 proteins:

  • NKX31_HUMAN
genes like me logo Genes that share paralogs with NKX3-1: view

Variants for NKX3-1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NKX3-1 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
709245 Benign: not provided 23,681,395(-) A/G SYNONYMOUS_VARIANT
721025 Benign: not provided 23,681,332(-) C/T SYNONYMOUS_VARIANT
rs2228013 - p.Arg52Cys

Additional dbSNP identifiers (rs#s) for NKX3-1 Gene

Structural Variations from Database of Genomic Variants (DGV) for NKX3-1 Gene

Variant ID Type Subtype PubMed ID
nsv1028341 CNV gain 25217958
nsv831269 CNV gain 17160897

Variation tolerance for NKX3-1 Gene

Residual Variation Intolerance Score: 60.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.85; 48.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKX3-1 Gene

Human Gene Mutation Database (HGMD)
NKX3-1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NKX3-1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX3-1 Gene

Disorders for NKX3-1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for NKX3-1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
prostatitis
chromosome 8p deletion
  • 8p deletion
prostate cancer
  • prostate cancer, somatic
nephrogenic adenoma
  • nephrogenic metaplasia
rete testis neoplasm
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NKX3-1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with NKX3-1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NKX3-1 Gene

Publications for NKX3-1 Gene

  1. A novel human prostate-specific, androgen-regulated homeobox gene (NKX3.1) that maps to 8p21, a region frequently deleted in prostate cancer. (PMID: 9226374) He WW … Carter KC (Genomics 1997) 2 3 4 23
  2. Gene expression profiles in the PC-3 human prostate cancer cells induced by NKX3.1. (PMID: 19462257) Zhang P … Jiang A (Molecular biology reports 2010) 3 4 23
  3. Purification and identification of a novel complex which is involved in androgen receptor-dependent transcription. (PMID: 12972618) Hosohata K … Wang Z (Molecular and cellular biology 2003) 3 4 23
  4. Full-length cDNA sequence and genomic organization of human NKX3A - alternative forms and regulation by both androgens and estrogens. (PMID: 11137288) Korkmaz KS … Saatcioglu F (Gene 2000) 3 4 23
  5. Isolation and androgen regulation of the human homeobox cDNA, NKX3.1. (PMID: 9537602) Prescott JL … Tindall DJ (The Prostate 1998) 3 4 23

Products for NKX3-1 Gene

Sources for NKX3-1 Gene