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Aliases for NKX6-3 Gene

Aliases for NKX6-3 Gene

  • NK6 Homeobox 3 2 3 5
  • NK6 Transcription Factor Related, Locus 3 (Drosophila) 2
  • NK6 Transcription Factor Related, Locus 3 3
  • Homeobox Protein Nkx-6.3 3
  • NKX6.3 3

External Ids for NKX6-3 Gene

Previous GeneCards Identifiers for NKX6-3 Gene

  • GC08M041503
  • GC08M040031

Summaries for NKX6-3 Gene

Entrez Gene Summary for NKX6-3 Gene

  • The NKX family of homeodomain proteins controls numerous developmental processes. Members of the NKX6 subfamily, including NKX6-3, are involved in development of the central nervous system (CNS), gastrointestinal tract, and pancreas (Alanentalo et al., 2006 [PubMed 16326147]).[supplied by OMIM, Mar 2008]

GeneCards Summary for NKX6-3 Gene

NKX6-3 (NK6 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 NKX6-1.

UniProtKB/Swiss-Prot for NKX6-3 Gene

  • Putative transcription factor, which may be involved in patterning of central nervous system and pancreas.

Additional gene information for NKX6-3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NKX6-3 Gene

Genomics for NKX6-3 Gene

GeneHancer (GH) Regulatory Elements for NKX6-3 Gene

Promoters and enhancers for NKX6-3 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
GH08I041645 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 550.8 +4.3 4271 2.6 GLIS1 CEBPB CTBP2 KDM1A EBF1 ZIC2 SPI1 RELA EZH2 NKX6-3 PIR46434
GH08I041577 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 9.7 +72.2 72203 2.5 HDGF ARID4B SIN3A DMAP1 ZNF766 ZNF143 ZNF207 SP3 ZHX2 REST GPAT4 LOC102723729 IKBKB KAT6A ENSG00000254165 NKX6-3 GOLGA7 PIR42833
GH08I041612 Enhancer 0.8 ENCODE 21.8 +37.8 37772 1.2 HDGF DRAP1 CTCF RB1 ETV1 ARID4B MAX ZNF2 RAD21 RARA NKX6-3 ENSG00000253174 GINS4 LOC102723729 GPAT4 ENSG00000253389 PIR42833 ENSG00000264578
GH08I041609 Enhancer 0.7 ENCODE 22.9 +40.7 40679 1.9 FOXA2 USF1 MAX RAD21 YY1 TEAD3 POLR2A SCRT2 GATAD2A RXRA PIR42833 NKX6-3 GPAT4 ENSG00000253174 GINS4 LOC102723729 ENSG00000264578
GH08I041621 Enhancer 0.7 ENCODE 11.9 +27.9 27949 2.1 HDGF EBF1 BATF KLF5 IRF4 CTBP1 POLR2A NFATC1 ZNF207 NR2F6 ENSG00000264578 PIR46434 NKX6-3 GPAT4 ENSG00000253389
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NKX6-3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NKX6-3 gene promoter:

Genomic Locations for NKX6-3 Gene

Genomic Locations for NKX6-3 Gene
5,492 bases
Minus strand

Genomic View for NKX6-3 Gene

Genes around NKX6-3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX6-3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX6-3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX6-3 Gene

Proteins for NKX6-3 Gene

  • Protein details for NKX6-3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Nkx-6.3
    Protein Accession:
    Secondary Accessions:
    • Q96LR0

    Protein attributes for NKX6-3 Gene

    265 amino acids
    Molecular mass:
    28948 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for NKX6-3 Gene


neXtProt entry for NKX6-3 Gene

Post-translational modifications for NKX6-3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX6-3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NKX6-3 Gene

Domains & Families for NKX6-3 Gene

Gene Families for NKX6-3 Gene

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

Protein Domains for NKX6-3 Gene

Suggested Antigen Peptide Sequences for NKX6-3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NKX6-3: view

No data available for UniProtKB/Swiss-Prot for NKX6-3 Gene

Function for NKX6-3 Gene

Molecular function for NKX6-3 Gene

UniProtKB/Swiss-Prot Function:
Putative transcription factor, which may be involved in patterning of central nervous system and pancreas.

Phenotypes From GWAS Catalog for NKX6-3 Gene

Gene Ontology (GO) - Molecular Function for NKX6-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IDA 28473536
genes like me logo Genes that share ontologies with NKX6-3: view

Phenotypes for NKX6-3 Gene

genes like me logo Genes that share phenotypes with NKX6-3: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NKX6-3 Gene

Localization for NKX6-3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX6-3 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 NKX6-3 gene
Compartment Confidence
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for NKX6-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with NKX6-3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NKX6-3 Gene

Pathways & Interactions for NKX6-3 Gene

SuperPathways for NKX6-3 Gene

No Data Available

Interacting Proteins for NKX6-3 Gene

Gene Ontology (GO) - Biological Process for NKX6-3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 26314965
genes like me logo Genes that share ontologies with NKX6-3: view

No data available for Pathways by source and SIGNOR curated interactions for NKX6-3 Gene

Drugs & Compounds for NKX6-3 Gene

No Compound Related Data Available

Transcripts for NKX6-3 Gene

mRNA/cDNA for NKX6-3 Gene

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

Unigene Clusters for NKX6-3 Gene

NK6 homeobox 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NKX6-3 Gene

No ASD Table

Relevant External Links for NKX6-3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NKX6-3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NKX6-3 Gene

mRNA differential expression in normal tissues according to GTEx for NKX6-3 Gene

This gene is overexpressed in Brain - Cerebellum (x15.7), Brain - Cerebellar Hemisphere (x15.0), and Stomach (x5.4).

SOURCE GeneReport for Unigene cluster for NKX6-3 Gene:


Evidence on tissue expression from TISSUES for NKX6-3 Gene

  • Nervous system(4.2)
  • Stomach(2.4)
genes like me logo Genes that share expression patterns with NKX6-3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX6-3 Gene

Orthologs for NKX6-3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NKX6-3 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia NKX6-3 34
  • 76 (a)
(Pan troglodytes)
Mammalia NKX6-3 34
  • 37 (a)
(Mus musculus)
Mammalia Nkx6-3 34
  • 36 (a)
(Bos Taurus)
Mammalia NKX6-3 34
  • 35 (a)
(Monodelphis domestica)
Mammalia NKX6-3 34
  • 34 (a)
(Ornithorhynchus anatinus)
Mammalia NKX6-3 34
  • 34 (a)
(Gallus gallus)
Aves NKX6-3 34
  • 32 (a)
(Anolis carolinensis)
Reptilia NKX6-3 34
  • 81 (a)
(Danio rerio)
Actinopterygii nkx6.3 34
  • 25 (a)
fruit fly
(Drosophila melanogaster)
Insecta NK7.1 34
  • 6 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 10 (a)
Species where no ortholog for NKX6-3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NKX6-3 Gene

Gene Tree for NKX6-3 (if available)
Gene Tree for NKX6-3 (if available)

Paralogs for NKX6-3 Gene

Paralogs for NKX6-3 Gene

(7) SIMAP similar genes for NKX6-3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NKX6-3: view

Variants for NKX6-3 Gene

Sequence variations from dbSNP and Humsavar for NKX6-3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000170234 -- 41,645,285(-) C/A 3_prime_UTR_variant
rs1000201546 -- 41,645,570(-) T/C 3_prime_UTR_variant
rs1000537329 -- 41,647,008(-) G/C intron_variant
rs1000732205 -- 41,650,361(-) G/A/C/T coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant
rs1001373457 -- 41,650,731(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NKX6-3 Gene

Variant ID Type Subtype PubMed ID
esv3576565 CNV gain 25503493
nsv831299 CNV loss 17160897

Variation tolerance for NKX6-3 Gene

Residual Variation Intolerance Score: 77.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.09; 38.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKX6-3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX6-3 Gene

Disorders for NKX6-3 Gene

Additional Disease Information for NKX6-3

No disorders were found for NKX6-3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NKX6-3 Gene

Publications for NKX6-3 Gene

  1. Cloning and analysis of Nkx6.3 during CNS and gastrointestinal development. (PMID: 16326147) Alanentalo T … Ahlgren U (Gene expression patterns : GEP 2006) 2 3 58
  2. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3 58
  3. Inactivation of NKX6.3 in the stomach leads to abnormal expression of CDX2 and SOX2 required for gastric-to-intestinal transdifferentiation. (PMID: 26743476) Yoon JH … Park WS (Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2016) 3 58
  4. NKX6.3 Is a Transcription Factor for Wnt/β-catenin and Rho-GTPase Signaling-Related Genes to Suppress Gastric Cancer Progression. (PMID: 27333045) Yoon JH … Park WS (EBioMedicine 2016) 3 58
  5. NKX6.3 controls gastric differentiation and tumorigenesis. (PMID: 26314965) Yoon JH … Park WS (Oncotarget 2015) 3 58

Products for NKX6-3 Gene

Sources for NKX6-3 Gene

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