Human Gene NKX3-1 (ENST00000523261.1) Description and Page Index
  Description: Homo sapiens NK3 homeobox 1 (NKX3-1), transcript variant 2, mRNA. (from RefSeq NM_001256339)
RefSeq Summary (NM_001256339): 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].
Gencode Transcript: ENST00000523261.1
Gencode Gene: ENSG00000167034.10
Transcript (Including UTRs)
   Position: hg38 chr8:23,680,988-23,682,889 Size: 1,902 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr8:23,681,221-23,682,889 Size: 1,669 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr8:23,680,988-23,682,889)mRNA (may differ from genome)Protein (159 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein Nkx-3.1; AltName: Full=Homeobox protein NK-3 homolog A;
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.
SUBUNIT: 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.
INTERACTION: P11387:TOP1; NbExp=6; IntAct=EBI-1385894, EBI-876302;
TISSUE SPECIFICITY: Highly expressed in the prostate and, at a lower level, in the testis.
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.
PTM: Ubiquitinated by TOPORS; monoubiquitinated at several residues and also polyubiquitinated on single residues.
SIMILARITY: Belongs to the NK-3 homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: NKX3-1
Diseases sorted by gene-association score: chromosome 8p deletion (18), prostate cancer (14), urethral diverticulum (9), prostatitis (8), male reproductive organ cancer (7), prostate sarcoma (7), reproductive organ cancer (2), prostate cancer susceptibility (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 118.55 RPKM in Prostate
Total median expression: 191.22 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -53.00233-0.227 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help


ModBase Predicted Comparative 3D Structure on Q99801
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000983 transcription factor activity, RNA polymerase II core promoter sequence-specific
GO:0001047 core promoter binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0004882 androgen receptor activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0030284 estrogen receptor activity
GO:0030295 protein kinase activator activity
GO:0030331 estrogen receptor binding
GO:0042826 histone deacetylase binding
GO:0043565 sequence-specific DNA binding
GO:0043621 protein self-association
GO:0044212 transcription regulatory region DNA binding
GO:0097162 MADS box domain binding
GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process

Biological Process:
GO:0001655 urogenital system development
GO:0001656 metanephros development
GO:0001756 somitogenesis
GO:0001934 positive regulation of protein phosphorylation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007275 multicellular organism development
GO:0007431 salivary gland development
GO:0007507 heart development
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0008584 male gonad development
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010942 positive regulation of cell death
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling
GO:0030521 androgen receptor signaling pathway
GO:0030850 prostate gland development
GO:0032147 activation of protein kinase activity
GO:0033574 response to testosterone
GO:0035690 cellular response to drug
GO:0035907 dorsal aorta development
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043491 protein kinase B signaling
GO:0043569 negative regulation of insulin-like growth factor receptor signaling pathway
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045930 negative regulation of mitotic cell cycle
GO:0045931 positive regulation of mitotic cell cycle
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048754 branching morphogenesis of an epithelial tube
GO:0050680 negative regulation of epithelial cell proliferation
GO:0051781 positive regulation of cell division
GO:0060037 pharyngeal system development
GO:0060442 branching involved in prostate gland morphogenesis
GO:0060664 epithelial cell proliferation involved in salivary gland morphogenesis
GO:0060770 negative regulation of epithelial cell proliferation involved in prostate gland development
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor
GO:0071383 cellular response to steroid hormone stimulus
GO:0071456 cellular response to hypoxia
GO:0071850 mitotic cell cycle arrest
GO:0071899 negative regulation of estrogen receptor binding
GO:2000836 positive regulation of androgen secretion
GO:2001022 positive regulation of response to DNA damage stimulus
GO:2001235 positive regulation of apoptotic signaling pathway
GO:2001244 positive regulation of intrinsic apoptotic signaling pathway

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  LP896517 - Sequence 1381 from Patent EP3253886.
AF247704 - Homo sapiens homeobox protein NKX3.1 mRNA, complete cds.
BC111569 - Homo sapiens cDNA clone IMAGE:40053523.
BC111574 - Homo sapiens cDNA clone IMAGE:40053531.
U80669 - Homo sapiens androgen regulated homeobox protein (NKX3.1) mRNA, complete cds.
AF249672 - Homo sapiens homeodomain protein NKX3.1 isoform v4 (NKX3A) mRNA, complete cds; alternatively spliced.
AF249671 - Homo sapiens homeodomain protein NKX3.1 isoform v3 (NKX3A) mRNA, complete cds; alternatively spliced.
AF249670 - Homo sapiens homeodomain protein NKX3.1 isoform v2 (NKX3A) mRNA, complete cds; alternatively spliced.
JD515539 - Sequence 496563 from Patent EP1572962.
BC074863 - Homo sapiens NK3 homeobox 1, mRNA (cDNA clone MGC:104021 IMAGE:30915465), complete cds.
BC074864 - Homo sapiens NK3 homeobox 1, mRNA (cDNA clone MGC:103847 IMAGE:30915229), complete cds.
AF249669 - Homo sapiens homeodomain protein NKX3.1 isoform v1 (NKX3A) mRNA, complete cds; alternatively spliced.
U91540 - Human prostate-specific, androgen-regulated homeoprotein NKX3.1 mRNA, complete cds.
EU446642 - Synthetic construct Homo sapiens clone IMAGE:100070117; IMAGE:100011851; FLH257421.01L NK3 homeobox 1 (NKX3-1) gene, encodes complete protein.
AB464643 - Synthetic construct DNA, clone: pF1KB8902, Homo sapiens NKX3-1 gene for NK3 homeobox 1, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05200 - Pathways in cancer
hsa05215 - Prostate cancer

-  Other Names for This Gene
  Alternate Gene Symbols: NKX3.1, NKX31_HUMAN, NKX3A, NM_001256339, O15465, Q99801, Q9H2P4, Q9H2P5, Q9H2P6, Q9H2P7, Q9HBG0, uc031tao.1, uc031tao.2
UCSC ID: uc031tao.2
RefSeq Accession: NM_001256339
Protein: Q99801 (aka NKX31_HUMAN or NK31_HUMAN)
CCDS: CCDS59095.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.