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NKX2-4 Gene

protein-coding   GIFtS: 39
GCID: GC20M021371

NK2 Homeobox 4

(Previous names: NK-2 (Drosophila) homolog D, NK2 transcription factor related,...)
(Previous symbol: NKX2D)
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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
NK2 Homeobox 41 2     Homeobox Protein Nkx-2.42
NKX2D1 2 3 5     NK2 Transcription Factor Homolog D2
NK-2 (Drosophila) Homolog D1     NK2 Transcription Factor Related, Locus 42
NK2 Transcription Factor Related, Locus 4 (Drosophila)1     Homeobox Protein NK-2 Homolog D3
NKX2.42     

External Ids:    HGNC: 78371   Entrez Gene: 6445242   Ensembl: ENSG000001258167   OMIM: 6078085   UniProtKB: Q9H2Z43   

Export aliases for NKX2-4 gene to outside databases

Previous GC identifers: GC20U990020 GC20M021324


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NKX2-4 Gene:
NKX2-4 (NK2 homeobox 4) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is NKX2-1.

UniProtKB/Swiss-Prot: NKX24_HUMAN, Q9H2Z4
Function: Probable transcription factor




(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_000020.10  NC_018931.2  NT_011387.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the NKX2-4 gene promoter:
         Egr-2   Egr-3   FOXF2   p53   ARP-1   CUTL1   LCR-F1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NKX2-4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NKX2-4


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

Entrez Gene cytogenetic band: 20p11.22   Ensembl cytogenetic band:  20p11.22   HGNC cytogenetic band: 20p11.22

NKX2-4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NKX2-4 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M021371:  view genomic region     (about GC identifiers)

Start:
21,376,005 bp from pter      End:
21,378,666 bp from pter
Size:
2,662 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: NKX24_HUMAN, Q9H2Z4 (See protein sequence)
Recommended Name: Homeobox protein Nkx-2.4  
Size: 354 amino acids; 36179 Da
Secondary accessions: Q5VZV8

Explore the universe of human proteins at neXtProt for NKX2-4: NX_Q9H2Z4

Explore proteomics data for NKX2-4 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NKX2-4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_149416.1  
    ENSEMBL proteins: 
     ENSP00000345147  

    NKX2-4 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for NKX2-4

     
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    Cloud-Clone Corp. ELISAs for NKX2-4
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    Search eBioscience for ELISAs for NKX2-4 


    (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

    4 InterPro protein domains:
     IPR020479 Homeobox_metazoa
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q9H2Z4

    ProtoNet protein and cluster: Q9H2Z4

    UniProtKB/Swiss-Prot: NKX24_HUMAN, Q9H2Z4
    Similarity: Belongs to the NK-2 homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    Find genes that share domains with NKX2-4           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: NKX24_HUMAN, Q9H2Z4
    Function: Probable transcription factor

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding IEA--
         
    Find genes that share ontologies with NKX2-4           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NKX2-4
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    miRNA
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    Block miRNA regulation of human, mouse, rat NKX2-4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NKX2-4 (see all 14):
    hsa-miR-320a hsa-miR-92a hsa-miR-409-3p hsa-miR-25 hsa-miR-367 hsa-miR-320d hsa-miR-32 hsa-miR-320b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat NKX2-4

    Gene Editing
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    Clone
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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NKX2-4
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKX2-4


    (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
    NKX24_HUMAN, Q9H2Z4: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IEA--

    Find genes that share ontologies with NKX2-4           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 NKX2-4
    Interactions:

        Search GeneGlobe Interaction Network for NKX2-4

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for NKX2-4 (ENSP000003451474) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NCOA3ENSP000003610664STRING: ENSP00000361066
    RARAENSP000002540664STRING: ENSP00000254066
    GATA6ENSP000002692164STRING: ENSP00000269216
    GSX1ENSP000003043314STRING: ENSP00000304331
    GSX2ENSP000003191184STRING: ENSP00000319118
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0007275multicellular organismal development IEA--
    GO:0008150biological_process ND--

    Find genes that share ontologies with NKX2-4           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 NKX2-4 (NKX24)



    (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 NKX2-4 gene: 
    NM_033176.1  

    Unigene Cluster for NKX2-4:

    NK2 homeobox 4
    Hs.456662  [show with all ESTs]
    Unigene Representative Sequence: NM_033176
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000351817(uc010gcz.3)
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat NKX2-4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NKX2-4 (see all 14):
    hsa-miR-320a hsa-miR-92a hsa-miR-409-3p hsa-miR-25 hsa-miR-367 hsa-miR-320d hsa-miR-32 hsa-miR-320b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
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    Predesigned siRNA for gene silencing in human, mouse, rat NKX2-4
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: NKX2-4 (NM_033176)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NKX2-4
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat NKX2-4
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for NKX2-4
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NKX2-4
      QuantiTect SYBR Green Assays in human, mouse, rat NKX2-4
      QuantiFast Probe-based Assays in human, mouse, rat NKX2-4

    1 DOTS entry:

    DT.100749639 

    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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    NKX2-4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATCCACCTGA
    NKX2-4 Expression
    About this image


    NKX2-4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Thymus (Hematopoietic System)
             Thymus
     
     Lung (Respiratory System)
             Stem Bronchi
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
    NKX2-4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NKX2-4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.456662
        Custom PCR Arrays for NKX2-4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKX2-4

    (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 NKX2-4 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nkx2-41 , 5 NK2 transcription factor related, locus 4 (Drosophila)5
    NK2 homeobox 41
    90.38(n)1
    92.86(a)1
      2 (72.63 cM)5
    2287311  NM_023504.11  NP_075993.11 
     1470833165 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    47(a)
    many ↔ many
    LGf(4247110-4253138)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia nkx2-41 NK2 homeobox 4 68.23(n)
    70(a)
      100495653  XM_002939432.2  XP_002939478.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1715311 zgc:171531 66.56(n)
    69.37(a)
      562300  NM_001111166.1  NP_001104636.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta scro1 scarecrow 51.2(n)
    56.54(a)
      3355151  NM_001015473.2  NP_001015473.1 
    worm
    (Caenorhabditis elegans)
    Secernentea ceh-246
    Protein CEH-24 (ceh-24) mRNA, complete cds
    32(a)
    1 → many
    V(13813309-13815272) WBGene00000447


    ENSEMBL Gene Tree for NKX2-4 (if available)
    TreeFam Gene Tree for NKX2-4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NKX2-4 gene
    NKX2-12  NKX6-12  HMX32  TLX22  NKX3-12  TLX12  NKX2-32  HMX22  
    NKX6-32  NKX3-22  NKX6-22  NKX2-62  NKX2-82  NKX2-52  NKX2-22  HMX12  
    TLX32  
    7 SIMAP similar genes for NKX2-4 using alignment to 1 protein entry:     NKX24_HUMAN:
    HLX    NKX2-8    NKX2-1    NKX2-3    NKX2-2    NKX2-5
    NKX2-6

    Find genes that share paralogs with NKX2-4           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 NKX2-4 (see all 72)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1898773241,2
    --21375663(+) TTCTTC/GTTGTC 1 -- ds50010--------
    rs1922160401,2
    --21375680(+) TGAATA/GTAGAT 1 -- ds50010--------
    rs1840039731,2
    --21375820(+) CTCAGC/TTGATG 1 -- ds50010--------
    rs60358681,2
    C,F,A,H--21375826(+) TGATGC/TTGGGA 1 -- ds500128Minor allele frequency- T:0.46NS EA NA WA CSA 2768
    rs60474231,2
    C,F,A,H--21375909(+) TTTAGG/CGTAAC 1 -- ds500115Minor allele frequency- C:0.07NS EA WA NA CSA 662
    rs792953801,2
    C,F--21375915(+) GTAACA/GTACAA 1 -- ds50011Minor allele frequency- G:0.06EA 120
    rs1886846361,2
    --21375931(+) CACTTA/GCCAAA 1 -- ds50010--------
    rs1999641051,2
    C--21376894(+) TACCGG/ATGGTT 2 /H syn11Minor allele frequency- A:0.00EU 1031
    rs1814223401,2
    C--21376915(+) ATCTTC/GACCTG 2 V syn10--------
    rs1997476431,2
    --21377083(+) AGCGGA/GCCCAG 2 G syn10--------

    HapMap Linkage Disequilibrium report for NKX2-4 (21376005 - 21378666 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for NKX2-4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833941CNV Gain17160897
    nsv828702CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NKX2-4
    DNA2.0 Custom Variant and Variant Library Synthesis for NKX2-4

    (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: 607808    OMIM disorders: --


    Find genes that share disorders with NKX2-4           About GenesLikeMe


    Export disorders for NKX2-4 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 NKX2-4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with NKX2-4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Conserved linkage of NK-2 homeobox gene pairs Nkx2-2/2-4 and Nkx2- 1/2-9 in mammals. (PubMed id 10818213)1, 2, 3 Wang C.-C.... Harvey R.P. (Mamm. Genome 2000)
    2. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    3. Regional expression of the homeobox gene Nkx-2.2 in the developing mammalian forebrain. (PubMed id 1346742)1, 3 Price M....Di Lauro R. (Neuron 1992)

    (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: 644524 HGNC: 7837 Ensembl:ENSG00000125816 euGenes: HUgn644524 ECgene: NKX2-4
    H-InvDB: NKX2-4

    (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 NKX2-4 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 NKX2-4 gene:
    Search GeneIP for patents involving NKX2-4

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    (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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     QuantiFast Probe-based Assays in human, mouse, rat NKX2-4 QuantiTect SYBR Green Assays in human, mouse, rat NKX2-4
     Custom PCR Arrays for NKX2-4 Search Chromatin IP Primers for NKX2-4
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     Search Tocris compounds for NKX2-4 (NKX24)
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     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NKX2-4
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     Search Addgene for plasmids for NKX2-4
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