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Aliases for NKX2-3 Gene

Aliases for NKX2-3 Gene

  • NK2 Homeobox 3 2 3 5
  • Homeobox Protein NK-2 Homolog C 3 4
  • NKX2C 3 4
  • NK2 Transcription Factor Related, Locus 3 (Drosophila) 2
  • NK2 Transcription Factor Related, Locus 3 3
  • NK-2 (Drosophila) Homolog C 2
  • Homeobox Protein Nkx-2.3 3
  • NKX2.3 3
  • NKX4-3 3
  • NK2.3 3
  • NKX23 4
  • CSX3 3

External Ids for NKX2-3 Gene

Previous HGNC Symbols for NKX2-3 Gene

  • NKX2C

Previous GeneCards Identifiers for NKX2-3 Gene

  • GC10P100185
  • GC10P100526
  • GC10P101423
  • GC10P100957
  • GC10P101282
  • GC10P101292
  • GC10P094918

Summaries for NKX2-3 Gene

Entrez Gene Summary for NKX2-3 Gene

  • This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]

GeneCards Summary for NKX2-3 Gene

NKX2-3 (NK2 Homeobox 3) is a Protein Coding gene. Diseases associated with NKX2-3 include Crohn's Disease. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is NKX2-5.

UniProtKB/Swiss-Prot for NKX2-3 Gene

  • Transcription factor.

Gene Wiki entry for NKX2-3 Gene

Additional gene information for NKX2-3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NKX2-3 Gene

Genomics for NKX2-3 Gene

Regulatory Elements for NKX2-3 Gene

Enhancers for NKX2-3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H099617 1.4 ENCODE dbSUPER 11.2 +87.0 87002 5.6 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B CWF19L1 CHUK PHBP9 EBAG9P1 TPM4P1 SPCS2P2 ENSG00000231188 ENSG00000236308 DNMBP SLC25A28
GH10H099394 1.2 Ensembl ENCODE 10.1 -137.0 -136985 2.7 FOXA2 ATF1 ARID4B FEZF1 FOS PAF1 SP5 NFYC PPARG KAT8 LOC101927300 GOT1 CNNM1 NKX2-3 PIR44588
GH10H099391 1 Ensembl ENCODE 10.2 -140.2 -140209 2.2 CTCF SAP130 RB1 ZNF2 RAD21 TEAD3 SCRT2 SMC3 ZNF143 RUNX3 LOC101927300 GOT1 CNNM1 NKX2-3 PIR44588
GH10H099451 0.9 ENCODE 11.2 -81.8 -81775 0.2 ELF3 FOXA2 ARID4B FEZF1 RARA SCRT2 MIXL1 ZEB2 ZNF398 PPARG GOT1 NKX2-3 LOC101927300 GC10P099494
GH10H099707 1 ENCODE dbSUPER 10 +176.3 176252 3 LEF1 PKNOX1 BACH1 BATF ZNF644 ZNF316 ATF7 ZNF584 NFE2 ETV6 ENTPD7 GOT1 LOC101927300 NKX2-3 BLOC1S2 PIR43293 PIR46433
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NKX2-3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for NKX2-3 Gene

Genomic Locations for NKX2-3 Gene
3,592 bases
Plus strand

Genomic View for NKX2-3 Gene

Genes around NKX2-3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX2-3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX2-3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX2-3 Gene

Proteins for NKX2-3 Gene

  • Protein details for NKX2-3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Nkx-2.3
    Protein Accession:
    Secondary Accessions:
    • B4DUZ4
    • Q9NYS6

    Protein attributes for NKX2-3 Gene

    364 amino acids
    Molecular mass:
    38406 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH25788.1; Type=Miscellaneous discrepancy; Note=The lack of 97 nucleotides within coding exon 2 produces a frameshift and results in a truncated protein.; Evidence={ECO:0000305};

neXtProt entry for NKX2-3 Gene

Post-translational modifications for NKX2-3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX2-3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NKX2-3 Gene

Domains & Families for NKX2-3 Gene

Gene Families for NKX2-3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for NKX2-3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NK-2 homeobox family.
  • Belongs to the NK-2 homeobox family.
genes like me logo Genes that share domains with NKX2-3: view

Function for NKX2-3 Gene

Molecular function for NKX2-3 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor.

Phenotypes From GWAS Catalog for NKX2-3 Gene

Gene Ontology (GO) - Molecular Function for NKX2-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with NKX2-3: view
genes like me logo Genes that share phenotypes with NKX2-3: view

Animal Models for NKX2-3 Gene

MGI Knock Outs for NKX2-3:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NKX2-3 Gene

Localization for NKX2-3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX2-3 Gene

Subcellular locations from

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 NKX2-3 gene
Compartment Confidence
nucleus 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoli (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NKX2-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with NKX2-3: view

Pathways & Interactions for NKX2-3 Gene

SuperPathways for NKX2-3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NKX2-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001776 leukocyte homeostasis IEA --
GO:0002317 plasma cell differentiation IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006641 triglyceride metabolic process IEA --
genes like me logo Genes that share ontologies with NKX2-3: view

No data available for Pathways by source and SIGNOR curated interactions for NKX2-3 Gene

Drugs & Compounds for NKX2-3 Gene

No Compound Related Data Available

Transcripts for NKX2-3 Gene

mRNA/cDNA for NKX2-3 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NKX2-3 Gene

NK2 homeobox 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NKX2-3 Gene

No ASD Table

Relevant External Links for NKX2-3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NKX2-3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NKX2-3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NKX2-3 Gene

This gene is overexpressed in Colon - Sigmoid (x14.8), Spleen (x13.2), Small Intestine - Terminal Ileum (x8.7), Colon - Transverse (x6.8), and Minor Salivary Gland (x5.7).

Protein differential expression in normal tissues from HIPED for NKX2-3 Gene

This gene is overexpressed in Heart (38.6) and Fetal gut (26.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NKX2-3 Gene

Protein tissue co-expression partners for NKX2-3 Gene

SOURCE GeneReport for Unigene cluster for NKX2-3 Gene:


Evidence on tissue expression from TISSUES for NKX2-3 Gene

  • Spleen(4.4)
  • Intestine(4.3)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with NKX2-3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX2-3 Gene

Orthologs for NKX2-3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NKX2-3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NKX2-3 33 34
  • 99.27 (n)
(Canis familiaris)
Mammalia NKX2-3 34 33
  • 91.58 (n)
(Bos Taurus)
Mammalia NKX2-3 33 34
  • 91.48 (n)
(Mus musculus)
Mammalia Nkx2-3 33 16 34
  • 88.46 (n)
(Rattus norvegicus)
Mammalia Nkx2-3 33
  • 88 (n)
(Monodelphis domestica)
Mammalia NKX2-3 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia NKX2-3 34
  • 80 (a)
(Gallus gallus)
Aves NKX2-6 34
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nkx2-3 33
  • 64.23 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1046 33
(Danio rerio)
Actinopterygii nkx2.3 33 34
  • 57.63 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta tin 34
  • 20 (a)
(Caenorhabditis elegans)
Secernentea ceh-28 34
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HMRA1 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4350 34
  • 28 (a)
Species where no ortholog for NKX2-3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 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 NKX2-3 Gene

Gene Tree for NKX2-3 (if available)
Gene Tree for NKX2-3 (if available)

Paralogs for NKX2-3 Gene

(6) SIMAP similar genes for NKX2-3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NKX2-3: view

Variants for NKX2-3 Gene

Sequence variations from dbSNP and Humsavar for NKX2-3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs1000984923 -- 99,536,176(+) CCGAT(C/T)CTCTG utr-variant-3-prime
rs1001118418 -- 99,536,234(+) CAGCT(C/G)TCTCC utr-variant-3-prime
rs1001565485 -- 99,534,217(+) TGAGT(C/T)CGAGA intron-variant
rs1002275028 -- 99,531,465(+) GTCTC(C/T)TTCAG upstream-variant-2KB
rs1002300751 -- 99,532,905(+) TCTCC(A/C)GGACA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for NKX2-3 Gene

Variant ID Type Subtype PubMed ID
nsv831958 CNV gain 17160897

Variation tolerance for NKX2-3 Gene

Residual Variation Intolerance Score: 32.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.20; 24.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NKX2-3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX2-3 Gene

Disorders for NKX2-3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NKX2-3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
crohn's disease
  • crohn disease
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for NKX2-3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with NKX2-3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NKX2-3 Gene

Publications for NKX2-3 Gene

  1. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PMID: 22412388) Kenny EE … Peter I (PLoS genetics 2012) 3 45 60
  2. Analysis of 39 Crohn's disease risk loci in Swedish inflammatory bowel disease patients. (PMID: 19760754) Törkvist L … Pettersson S (Inflammatory bowel diseases 2010) 3 45 60
  3. Genetic analysis in a Dutch study sample identifies more ulcerative colitis susceptibility loci and shows their additive role in disease risk. (PMID: 19861958) Festen EA … Weersma RK (The American journal of gastroenterology 2010) 3 45 60
  4. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. (PMID: 20228799) McGovern DP … Seielstad M (Nature genetics 2010) 3 45 60
  5. Association between genome-wide association studies reported SNPs and pediatric-onset Crohn's disease in Canadian children. (PMID: 20473688) Amre DK … Levy E (Human genetics 2010) 3 45 60

Products for NKX2-3 Gene

Sources for NKX2-3 Gene

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