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NKX6-3 Gene

protein-coding   GIFtS: 40
GCID: GC08M041503

NK6 Homeobox 3

(Previous names: NK6 transcription factor related, locus 3 (Drosophila))
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
NK6 Homeobox 31 2
NKX6.32 5
NK6 Transcription Factor Related, Locus 3 (Drosophila)1
Homeobox Protein Nkx-6.32
NK6 Transcription Factor Related, Locus 32

External Ids:    HGNC: 263281   Entrez Gene: 1578482   Ensembl: ENSG000001650667   OMIM: 6107725   UniProtKB: A6NJ463   

Export aliases for NKX6-3 gene to outside databases

Previous GC identifers: GC08M041622 GC08M040031


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. GO annotations related to this gene include transcription regulatory region sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is NKX2-1.

UniProtKB/Swiss-Prot: NKX63_HUMAN, A6NJ46
Function: Putative transcription factor, which may be involved in patterning of central nervous system and
pancreas (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000008.10  NT_167187.2  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NKX6-3 gene promoter:
         C/EBPbeta   CP2   GATA-3   NF-kappaB2   NF-kappaB   ATF   Roaz   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNKX6-3 promoter sequence
   Search Chromatin IP Primers for NKX6-3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NKX6-3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 8p11.21   Ensembl cytogenetic band:  8p11.21   HGNC cytogenetic band: 8p11.21

NKX6-3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NKX6-3 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M041503:  view genomic region     (about GC identifiers)

Start:
41,502,697 bp from pter      End:
41,508,855 bp from pter
Size:
6,159 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NKX63_HUMAN, A6NJ46 (See protein sequence)
Recommended Name: Homeobox protein Nkx-6.3  
Size: 265 amino acids; 28948 Da
Secondary accessions: Q96LR0
Alternative splicing: 2 isoforms:  A6NJ46-1   A6NJ46-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NKX6-3: NX_A6NJ46

Explore proteomics data for NKX6-3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NKX6-3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689781.1  
    ENSEMBL proteins: 
     ENSP00000429553   ENSP00000428361  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    NKL: Homeoboxes / ANTP class : NKL subclass

    5 InterPro protein domains:
     IPR020479 Homeobox_metazoa
     IPR000047 HTH_motif
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry A6NJ46

    ProtoNet protein and cluster: A6NJ46

    UniProtKB/Swiss-Prot: NKX63_HUMAN, A6NJ46
    Similarity: Contains 1 homeobox DNA-binding domain


    Find genes that share domains with NKX6-3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NKX63_HUMAN, A6NJ46
    Function: Putative transcription factor, which may be involved in patterning of central nervous system and
    pancreas (By similarity)

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000976transcription regulatory region sequence-specific DNA binding IEA--
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding ----
         
    Find genes that share ontologies with NKX6-3           About GenesLikeMe


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Nkx6-3):
     digestive/alimentary  homeostasis/metabolism 

    Find genes that share phenotypes with NKX6-3           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Nkx6-3Nkx6-tm1Shiv for NKX6-3

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NKX6-3
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NKX6-3
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NKX6-3

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    1 qRT-PCR Assays for microRNA that regulate NKX6-3:
    hsa-miR-4271
    SwitchGear 3'UTR luciferase reporter plasmidNKX6-3 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat NKX6-3

    Gene Editing
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKX6-3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NKX63_HUMAN, A6NJ46: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with NKX6-3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NKX6-3
    Interactions:

        Search GeneGlobe Interaction Network for NKX6-3

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001709cell fate determination IEA--
    GO:0002067glandular epithelial cell differentiation IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0030857negative regulation of epithelial cell differentiation IEA--

    Find genes that share ontologies with NKX6-3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NKX6-3 (NKX63)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NKX6-3 gene: 
    NM_152568.2  

    Unigene Cluster for NKX6-3:

    NK6 homeobox 3
    Hs.647132
    Unigene Representative Sequence: NM_152568
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000524115(uc003xoa.2 uc010lxa.1) ENST00000518699
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat NKX6-3 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate NKX6-3:
    hsa-miR-4271
    SwitchGear 3'UTR luciferase reporter plasmidNKX6-3 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for NKX6-3
    Predesigned siRNA for gene silencing in human, mouse, rat NKX6-3
    Clone
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    GenScript: all cDNA clones in your preferred vector: NKX6-3 (NM_152568)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NKX6-3
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat NKX6-3
      QuantiFast Probe-based Assays in human, mouse, rat NKX6-3

    1 DOTS entry:

    DT.75199521 

    4 AceView cDNA sequences:

    AI969444 AK057898 NM_152568 D38706 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NKX6-3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCTTTCTGCT
    NKX6-3 Expression
    About this image


    NKX6-3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)
             Blimp1- mVenus and stella-ECFP genetically modified stem cells
     
     Brain (Nervous System)
             Medulla Oblongata
    NKX6-3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NKX6-3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.647132
        Custom PCR Arrays for NKX6-3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKX6-3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for NKX6-3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nkx6-35 NK6 homeobox 3   --   8 (11.42 cM) 23153271 
    chicken
    (Gallus gallus)
    Aves NKX6-36
    NK6 homeobox 3
    32(a)
    1 ↔ 1
    22(2609090-2610953)
    lizard
    (Anolis carolinensis)
    Reptilia NKX6-36
    NK6 homeobox 3
    81(a)
    1 ↔ 1
    GL343578.1(405283-405513)
    zebrafish
    (Danio rerio)
    Actinopterygii nkx6.36
    NK6 homeobox 3
    25(a)
    1 ↔ 1
    8(39503632-39506306) ENSDARG00000060529
    fruit fly
    (Drosophila melanogaster)
    Insecta NK7.16
    NK7.1
    6(a)
    many ↔ many
    3R(10155862-10198673)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NKX6-3 gene
    NKX2-12  NKX6-12  HMX32  TLX22  NKX3-12  TLX12  NKX2-32  HMX22  
    NKX3-22  NKX6-22  NKX2-62  NKX2-82  NKX2-52  NKX2-22  NKX2-42  HMX12  
    TLX32  
    7 SIMAP similar genes for NKX6-3 using alignment to 1 protein entry:     NKX63_HUMAN:
    HMX2    HOXA4    HOXC13    NKX6-2    HOXB1    HLX
    POU6F1

    Find genes that share paralogs with NKX6-3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NKX6-3 (see all 80)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1409038901,2
    --41503431(+) GGTCTA/GAGGAG 1 -- ds50010--------
    rs7551621,2
    C,F,A,H--41503727(+) CTGTGC/ACTCCC 1 -- ds500117Minor allele frequency- A:0.37NA PA EA NS WA CSA 1271
    rs1498360061,2
    --41503741(+) TGGCCG/TCCTCC 1 -- ds50010--------
    rs58911651,2
    C--41503854(+) CATCC-/AAAG  
            
    AAAGA
    1 -- ut311Minor allele frequency- AAAG:0.00CSA 2
    rs30637331,2
    C--41503855(+) AAAGA-/AAGA  
            
    CTCAG
    1 -- ut310--------
    rs1442420851,2
    C--41503922(+) GGCGT-/CCCCCC 1 -- ut310--------
    rs588955041,2
    C--41503937(+) GGCTGC/AAGCCA 1 -- ut313Minor allele frequency- A:0.05CSA WA EA 240
    rs2001278951,2
    --41504007(+) AAGGCA/GGCGCG 2 A syn10--------
    rs1388157321,2
    C,F--41504012(+) GGCGCG/AGTGCT 2 /R /C mis11Minor allele frequency- A:0.00NA 4236
    rs2021955581,2
    C--41504043(+) TTCTCA/GTCGTC 2 D syn10--------

    HapMap Linkage Disequilibrium report for NKX6-3 (41502697 - 41508855 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for NKX6-3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831299CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NKX6-3
    DNA2.0 Custom Variant and Variant Library Synthesis for NKX6-3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 610772    OMIM disorders: --


    Find genes that share disorders with NKX6-3           About GenesLikeMe


    Export disorders for NKX6-3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NKX6-3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with NKX6-3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and analysis of Nkx6.3 during CNS and gastrointestinal development. (PubMed id 16326147)1, 3 Alanentalo T....Ahlgren U. (Gene Expr. Patterns 2006)
    2. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 157848 HGNC: 26328 AceView: FLJ25169 Ensembl:ENSG00000165066 euGenes: HUgn157848
    ECgene: NKX6-3 H-InvDB: NKX6-3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NKX6-3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NKX6-3 gene:
    Search GeneIP for patents involving NKX6-3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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