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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NKX2-4 Gene

protein-coding   GIFtS: 38
GCID: GC20M021371

NK2 Homeobox 4

(Previous names: NK-2 (Drosophila) homolog D, NK2 transcription factor related,...)
(Previous symbol: NKX2D)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for NKX2-4 Gene: 
NKX2-4 (NK2 homeobox 4) is a protein-coding gene. Diseases associated with NKX2-4 include thyroiditis. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.2  NT_011387.8  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for NKX2-4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: NKX24_HUMAN, Q9H2Z4 (See protein sequence)
Recommended Name: Homeobox protein Nkx-2.4  
Size: 354 amino acids; 36179 Da
Subcellular location: Nucleus (By similarity)
Secondary accessions: Q5VZV8

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

Explore proteomics data for NKX2-4 at MOPED 

NKX2-4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

NKX2-4 Protein Expression

REFSEQ proteins: NP_149416.1  
ENSEMBL proteins: 
 ENSP00000345147  

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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

NKX2-4 for ontologies           About GeneDecksing



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

4 InterPro protein domains:
 IPR020479 Homeobox_metazoa
 IPR017970 Homeobox_CS
 IPR001356 Homeodomain
 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


NKX2-4 for domains           About GeneDecksing


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

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

     Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    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--
     
NKX2-4 for ontologies           About GeneDecksing


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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NKX2-4

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for NKX2-4 (ENSP000003451474) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
NCOA3ENSP000003610664STRING: ENSP00000361066
RARAENSP000002540664STRING: ENSP00000254066
About this table

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

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

NKX2-4 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for NKX2-4 (NKX24)

Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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
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Inhib. RNA
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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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

NKX2-4 expression in normal human tissues (normalized intensities)      NKX2-4 embryonic expression: see
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 
 5/20 selected tissues (see all 20) fully expand
 
 Brain (Nervous System)    fully expand to see all 8 entries
         Thalamus
         ganglion/cranial   
 
 Neural Tube (Nervous System)    fully expand to see all 3 entries
         Metencephalon
 
 Limb (Muscoskeletal System)    fully expand to see all 2 entries
         limb/hindlimb   
 
 Peripheral Nervous System (Nervous System)
         spinal/ganglion/dorsal root ganglion   
 
 Lung (Respiratory System)
         Stem Bronchi

See NKX2-4 Protein Expression from SPIRE MOPED and PaxDB
SOURCE GeneReport for Unigene cluster: Hs.456662
    SABiosciences Custom PCR Arrays for NKX2-4
Primer
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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)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for NKX2-4 gene from 5/8 species (see all 8)    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)1, 5 92.45(n)1
95.7(a)1
  2 (72.63 cM)5
2287311  NM_023504.11  NP_075993.11 
 1470833165 
lizard
(Anolis carolinensis)
Reptilia --
--
37(a)
possible ortholog
LGf(4247110-4253138)
zebrafish
(Danio rerio)
Actinopterygii zgc:1715311 zgc:171531 68.96(n)
72.5(a)
  562300  NM_001111166.1  NP_001104636.1 
fruit fly
(Drosophila melanogaster)
Insecta scro6
scarecrow
26(a)
1 → many
3LHet(207493-252455)
worm
(Caenorhabditis elegans)
Secernentea ceh-246
ceh-276
Protein CEH-27, isoform a
27(a)
23(a)
possible ortholog
possible ortholog
V(13813309-13815272)
V(11661553-11664697)


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)
About This Section
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

NKX2-4 for paralogs           About GeneDecksing



(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/72 SNPs in NKX2-4 are shown (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

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 607808    OMIM disorders: --

2 diseases for NKX2-4:    About MalaCards
thyroiditis    


NKX2-4 for disorders           About GeneDecksing


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)
About This Section

PubMed articles for NKX2-4 gene integrated from 9 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. (2000)
  2. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
  3. Regional expression of the homeobox gene Nkx-2.2 in t he developing mammalian forebrain. (PubMed id 1346742)1, 3 Price M....Di Lauro R. (1992)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 644524 HGNC: 7837 Ensembl:ENSG00000125816 euGenes: HUgn644524 ECgene: NKX2-4
H-InvDB: NKX2-4

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
Patent Information for NKX2-4 gene:
Search GeneIP for patents involving NKX2-4

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 inGenious Targeting Laboratory - Custom generated mouse model solutions for NKX2-4
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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