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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. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is NKX2-6.

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

GeneHancer (GH) Regulatory Elements for NKX2-3 Gene

Promoters and enhancers for NKX2-3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J099525 Enhancer 1.2 Ensembl ENCODE dbSUPER 650.7 -0.3 -264 13.6 CTCF USF1 ZBTB6 SUZ12 ZNF140 BMI1 ETS1 ZNF335 ZNF664 E2F1 LINC01475 NKX2-3 EBAG9P1 PHBP9 ENSG00000236308 SLC25A28 DNMBP ENSG00000228778 GC10P099494
GH10J099617 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.2 +87.0 87001 5.6 ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC ZNF610 GLIS1 NBN NR2C1 SLC25A28 ENSG00000260475 CWF19L1 PHBP9 CHUK DNMBP EBAG9P1 TPM4P1 SPCS2P2 ENSG00000231188
GH10J099394 Enhancer 1.1 Ensembl ENCODE 10.1 -137.0 -136985 2.7 FOXA2 ARID4B FEZF1 ZNF48 ETS1 FOS NFKBIZ PAF1 RXRA SP5 LOC101927300 SLC25A28 GOT1 CNNM1 NKX2-3 PIR44588
GH10J099707 Enhancer 1 ENCODE dbSUPER 10 +176.3 176251 3 PKNOX1 STAT5A BATF IRF4 ZFP91 ATF7 BCLAF1 IKZF2 RUNX3 CREM PIR46681 PIR43293 ENTPD7 NKX2-3 LOC101927300 GOT1 BLOC1S2 GC10M099706 PIR46433 CUTC
GH10J099391 Enhancer 0.9 Ensembl ENCODE 10.2 -140.2 -140208 2.2 CTCF SAP130 RB1 ZNF2 RAD21 TEAD3 SCRT2 SMC3 ZNF143 ZNF444 LOC101927300 GOT1 CNNM1 NKX2-3 PIR44588
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

Top Transcription factor binding sites by QIAGEN in the NKX2-3 gene promoter:
  • Nkx2-5
  • E2F-5
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • HSF2

Genomic Locations for NKX2-3 Gene

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

Antibody Products

  • Abcam antibodies for NKX2-3
  • Boster Bio Antibodies for NKX2-3
  • Santa Cruz Biotechnology (SCBT) Antibodies for NKX2-3

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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX2-3

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:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX2-3

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 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 34 33
  • 99.27 (n)
(Canis familiaris)
Mammalia NKX2-3 34 33
  • 91.58 (n)
(Bos Taurus)
Mammalia NKX2-3 34 33
  • 91.48 (n)
(Mus musculus)
Mammalia Nkx2-3 16 34 33
  • 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 34 33
  • 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)
Evolutionary constrained regions (ECRs) for NKX2-3: view image

Paralogs for NKX2-3 Gene

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 Variation AA Info Type
rs1000984923 -- 99,536,176(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1001118418 -- 99,536,234(+) G/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1001565485 -- 99,534,217(+) C/T intron_variant
rs1002275028 -- 99,531,465(+) T/C upstream_transcript_variant
rs1002300751 -- 99,532,905(+) C/A upstream_transcript_variant

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)

Additional Variant Information 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

Additional Disease Information for NKX2-3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for NKX2-3 Gene.

No data available for MalaCards , 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 44 58
  2. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. (PMID: 20228799) McGovern DP … Seielstad M (Nature genetics 2010) 3 44 58
  3. 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 44 58
  4. 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 44 58
  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 44 58

Products for NKX2-3 Gene

Sources for NKX2-3 Gene

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