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] See more...

Aliases for NKX6-3 Gene

Aliases for NKX6-3 Gene

  • NK6 Homeobox 3 2 3 5
  • Homeobox Protein Nkx-6.3 3 4
  • NK6 Transcription Factor Related, Locus 3 (Drosophila) 2
  • NK6 Transcription Factor Related, Locus 3 3
  • FLJ25169 2
  • NKX6.3 3
  • NKX6-3 5

External Ids for NKX6-3 Gene

Previous GeneCards Identifiers for NKX6-3 Gene

  • GC08M041622
  • 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 Summary for NKX6-3 Gene

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

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NKX6-3 Gene

Genomics for NKX6-3 Gene

GeneHancer (GH) Regulatory Elements Pubs


GeneHancers around NKX6-3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NKX6-3

Top Transcription factor binding sites by QIAGEN in the NKX6-3 gene promoter:
  • ATF
  • C/EBPbeta
  • CP2
  • GATA-3
  • NF-kappaB
  • NF-kappaB2
  • Roaz

Genomic Locations for NKX6-3 Gene

Latest Assembly
chr8:41,645,177-41,650,817
(GRCh38/hg38)
Size:
5,641 bases
Orientation:
Minus strand

Previous Assembly
chr8:41,502,696-41,508,336
(GRCh37/hg19 by Entrez Gene)
Size:
5,641 bases
Orientation:
Minus strand

chr8:41,502,697-41,508,855
(GRCh37/hg19 by Ensembl)
Size:
6,159 bases
Orientation:
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:
    A6NJ46-NKX63_HUMAN
    Recommended name:
    Homeobox protein Nkx-6.3
    Protein Accession:
    A6NJ46
    Secondary Accessions:
    • Q96LR0

    Protein attributes for NKX6-3 Gene

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

    Alternative splice isoforms for NKX6-3 Gene

    UniProtKB/Swiss-Prot:

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

Antibodies for research

  • Abcam antibodies for NKX6-3
  • Santa Cruz Biotechnology (SCBT) Antibodies for NKX6-3

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

Domains & Families for NKX6-3 Gene

Gene Families for NKX6-3 Gene

HGNC:
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:
  • Homeobox protein Nkx-6.3 (NKX63_HUMAN)
genes like me logo Genes that share domains with NKX6-3: view

No data available for Graphical View of Domain Structure and 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:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 26314965
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 26314965
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 26314965
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with NKX6-3: view
genes like me logo Genes that share phenotypes with NKX6-3: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX6-3

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

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 NKX6-3 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IBA 21873635
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

PathCards logo

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:0000122 negative regulation of transcription by RNA polymerase II IDA 26314965
GO:0001709 cell fate determination IEA --
GO:0002067 glandular epithelial cell differentiation IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
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 :
1 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX6-3

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
NKX6-3

Expression for NKX6-3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NKX6-3

SOURCE GeneReport for Unigene cluster for NKX6-3 Gene:

Hs.647132

Evidence on tissue expression from TISSUES for NKX6-3 Gene

  • Nervous system(4.3)
  • Stomach(2.6)
genes like me logo Genes that share expression patterns with NKX6-3: view

Primer products for research

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
Dog
(Canis familiaris)
Mammalia NKX6-3 30
  • 76 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia NKX6-3 30
  • 37 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Nkx6-3 30
  • 36 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia NKX6-3 30
  • 35 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NKX6-3 30
  • 34 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia NKX6-3 30
  • 34 (a)
OneToOne
Chicken
(Gallus gallus)
Aves NKX6-3 30
  • 32 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NKX6-3 30
  • 81 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii nkx6.3 30
  • 25 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta NK7.1 30
  • 6 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 10 (a)
OneToMany
Species where no ortholog for NKX6-3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for NKX6-3 (if available)
TreeFam:
Gene Tree for NKX6-3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKX6-3: view image
Alliance of Genome Resources:
Additional Orthologs for NKX6-3

Paralogs for NKX6-3 Gene

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

  • NKX63_HUMAN
genes like me logo Genes that share paralogs with NKX6-3: view

Variants for NKX6-3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NKX6-3 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs114744615 Benign: not provided 41,647,283(-) C/A
NM_001364841.2(NKX6-3):c.553-589G>T
MISSENSE_VARIANT,INTRON
rs74990493 Benign: not provided 41,646,701(-) T/A
NM_001364841.2(NKX6-3):c.553-7A>T
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NKX6-3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
NKX6-3
Leiden Open Variation Database (LOVD)
NKX6-3

SNP Genotyping and Copy Number Assays for research

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
  2. Genome-wide gene-based analyses of weight loss interventions identify a potential role for NKX6.3 in metabolism. (PMID: 30710084) Valsesia A … Hager J (Nature communications 2019) 3
  3. NKX6.3 protects against gastric mucosal atrophy by downregulating β-amyloid production. (PMID: 30686901) Yoon JH … Park WS (World journal of gastroenterology 2019) 3
  4. Multiple genetic mutations caused by NKX6.3 depletion contribute to gastric tumorigenesis. (PMID: 30514953) Yoon JH … Park WS (Scientific reports 2018) 3
  5. 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

Products for NKX6-3 Gene

Sources for NKX6-3 Gene