Aliases for NKX2-4 Gene

Aliases for NKX2-4 Gene

  • NK2 Homeobox 4 2 3 5
  • Homeobox Protein Nkx-2.4 3 4
  • NKX2.4 2 3
  • NKX2D 3 4
  • NK2 Transcription Factor Related, Locus 4 (Drosophila) 2
  • NK2 Transcription Factor Related, Locus 4 3
  • NK2 Transcription Factor Homolog D 3
  • Homeobox Protein NK-2 Homolog D 4
  • NK-2 (Drosophila) Homolog D 2
  • NKX2-4 5

External Ids for NKX2-4 Gene

Previous HGNC Symbols for NKX2-4 Gene

  • NKX2D

Previous GeneCards Identifiers for NKX2-4 Gene

  • GC20U990020
  • GC20M021324
  • GC20M021371

Summaries for NKX2-4 Gene

GeneCards Summary for NKX2-4 Gene

NKX2-4 (NK2 Homeobox 4) is a Protein Coding gene. Diseases associated with NKX2-4 include Diabetes Mellitus, Neonatal, With Congenital Hypothyroidism. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is NKX2-1.

UniProtKB/Swiss-Prot Summary for NKX2-4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NKX2-4 Gene

Genomics for NKX2-4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NKX2-4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J021396 Promoter 0.7 Ensembl 250.7 +0.6 625 1 GLIS1 ZFX ZBTB8A L3MBTL2 EGR2 EZH2 ZBTB17 ARNT ZFHX2 ZBTB26 ENSG00000225280 LOC105372558 NKX2-4 HSALNG0129108 XRN2
GH20J021090 Enhancer 1.3 UCNEbase Ensembl ENCODE 11.1 +306.9 306925 3.2 FEZF1 ZNF639 ZEB1 FOSL2 JUND PRDM6 INSM2 ZSCAN23 ZNF24 ZNF133 ENSG00000225280 NKX2-4 KIZ ENSG00000283405 HSALNG0129090 LINC00237 RALGAPA2
GH20J021322 Enhancer 1 Ensembl ENCODE 10.4 +72.5 72525 6.4 IKZF1 NFIC FEZF1 PRDM1 STAT3 TCF7L2 RBM22 NFE2 PRDM6 ATF1 ENSG00000225280 NKX2-4 KIZ RF00017-3188 lnc-KIZ-9 XRN2
GH20J021360 Enhancer 0.6 Ensembl ENCODE 11.3 +36.3 36325 2.8 CEBPB RBM22 PRDM6 SPI1 ARNT NKX2-4 ENSG00000225280 XRN2 KIZ RF00017-3191 HSALNG0129107
GH20J021214 Enhancer 0.6 Ensembl ENCODE 10 +182.0 182025 4.2 SP1 POU5F1 NANOG PHF8 KIZ ENSG00000225280 NKX2-4 KIZ-AS1 RPS15AP1 XRN2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NKX2-4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NKX2-4

Top Transcription factor binding sites by QIAGEN in the NKX2-4 gene promoter:
  • ARP-1
  • CUTL1
  • Egr-2
  • Egr-3
  • FOXF2
  • LCR-F1
  • p53

Genomic Locations for NKX2-4 Gene

Latest Assembly
chr20:21,395,365-21,397,526
(GRCh38/hg38)
Size:
2,162 bases
Orientation:
Minus strand

Previous Assembly
chr20:21,376,003-21,378,164
(GRCh37/hg19 by Entrez Gene)
Size:
2,162 bases
Orientation:
Minus strand

chr20:21,376,005-21,378,666
(GRCh37/hg19 by Ensembl)
Size:
2,662 bases
Orientation:
Minus strand

Genomic View for NKX2-4 Gene

Genes around NKX2-4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX2-4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX2-4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX2-4 Gene

Proteins for NKX2-4 Gene

  • Protein details for NKX2-4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H2Z4-NKX24_HUMAN
    Recommended name:
    Homeobox protein Nkx-2.4
    Protein Accession:
    Q9H2Z4
    Secondary Accessions:
    • Q5VZV8

    Protein attributes for NKX2-4 Gene

    Size:
    354 amino acids
    Molecular mass:
    36179 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NKX2-4 Gene

Post-translational modifications for NKX2-4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX2-4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for NKX2-4

No data available for DME Specific Peptides for NKX2-4 Gene

Domains & Families for NKX2-4 Gene

Gene Families for NKX2-4 Gene

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

Protein Domains for NKX2-4 Gene

Suggested Antigen Peptide Sequences for NKX2-4 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein NK-2 homolog D (NKX24_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H2Z4

UniProtKB/Swiss-Prot:

NKX24_HUMAN :
  • Belongs to the NK-2 homeobox family.
Family:
  • Belongs to the NK-2 homeobox family.
genes like me logo Genes that share domains with NKX2-4: view

Function for NKX2-4 Gene

Molecular function for NKX2-4 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor.

Phenotypes From GWAS Catalog for NKX2-4 Gene

Gene Ontology (GO) - Molecular Function for NKX2-4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with NKX2-4: view

Phenotypes for NKX2-4 Gene

genes like me logo Genes that share phenotypes with NKX2-4: view

miRNA for NKX2-4 Gene

miRTarBase miRNAs that target NKX2-4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX2-4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NKX2-4 Gene

Localization for NKX2-4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX2-4 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 NKX2-4 gene
Compartment Confidence
nucleus 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NKX2-4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005575 cellular_component ND --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with NKX2-4: view

Pathways & Interactions for NKX2-4 Gene

PathCards logo

SuperPathways for NKX2-4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NKX2-4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0008150 biological_process ND --
GO:0030154 cell differentiation IBA 21873635
genes like me logo Genes that share ontologies with NKX2-4: view

No data available for Pathways by source and SIGNOR curated interactions for NKX2-4 Gene

Drugs & Compounds for NKX2-4 Gene

No Compound Related Data Available

Transcripts for NKX2-4 Gene

mRNA/cDNA for NKX2-4 Gene

1 REFSEQ mRNAs :
1 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 NKX2-4

Alternative Splicing Database (ASD) splice patterns (SP) for NKX2-4 Gene

No ASD Table

Relevant External Links for NKX2-4 Gene

GeneLoc Exon Structure for
NKX2-4

Expression for NKX2-4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NKX2-4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NKX2-4 Gene

This gene is overexpressed in Testis (x26.7), Brain - Hypothalamus (x12.6), and Uterus (x6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NKX2-4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NKX2-4

SOURCE GeneReport for Unigene cluster for NKX2-4 Gene:

Hs.456662
genes like me logo Genes that share expression patterns with NKX2-4: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX2-4 Gene

Orthologs for NKX2-4 Gene

This gene was present in the common ancestor of animals.

Orthologs for NKX2-4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NKX2-4 29 30
  • 99.72 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NKX2-4 30
  • 94 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Nkx2-4 29 16 30
  • 90.38 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Nkx2-4 29
  • 89.88 (n)
Dog
(Canis familiaris)
Mammalia NKX2-4 29 30
  • 88.96 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NKX2-4 30
  • 73 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 47 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nkx2-4 29
  • 68.23 (n)
Zebrafish
(Danio rerio)
Actinopterygii nkx2.1a 30
  • 69 (a)
OneToMany
zgc:171531 29 30
  • 66.56 (n)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta scro 29 30
  • 51.2 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ceh-24 30
  • 32 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CS-TTF1 30
  • 27 (a)
OneToMany
Species where no ortholog for NKX2-4 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)
  • Chicken (Gallus gallus)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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)
  • Wheat (Triticum aestivum)

Evolution for NKX2-4 Gene

ENSEMBL:
Gene Tree for NKX2-4 (if available)
TreeFam:
Gene Tree for NKX2-4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKX2-4: view image
Alliance of Genome Resources:
Additional Orthologs for NKX2-4

Paralogs for NKX2-4 Gene

(7) SIMAP similar genes for NKX2-4 Gene using alignment to 1 proteins:

  • NKX24_HUMAN
genes like me logo Genes that share paralogs with NKX2-4: view

Variants for NKX2-4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NKX2-4 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
rs181422340 Benign: not provided 21,396,277(-) G/C
NM_033176.2(NKX2-4):c.699C>G (p.Val233=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NKX2-4 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 NKX2-4 Gene

Variant ID Type Subtype PubMed ID
nsv1143980 CNV deletion 24896259
nsv828702 CNV gain 20364138
nsv833941 CNV gain 17160897

Variation tolerance for NKX2-4 Gene

Gene Damage Index Score: 0.55; 11.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKX2-4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NKX2-4
Leiden Open Variation Database (LOVD)
NKX2-4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX2-4 Gene

Disorders for NKX2-4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NKX2-4 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NKX2-4

genes like me logo Genes that share disorders with NKX2-4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NKX2-4 Gene

Publications for NKX2-4 Gene

  1. Conserved linkage of NK-2 homeobox gene pairs Nkx2-2/2-4 and Nkx2-1/2-9 in mammals. (PMID: 10818213) Wang CC … Harvey RP (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 2 3 4
  2. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4
  3. Regional expression of the homeobox gene Nkx-2.2 in the developing mammalian forebrain. (PMID: 1346742) Price M … Di Lauro R (Neuron 1992) 2 3
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes via Histone Deacetylation. (PMID: 29844126) Weissmann S … Helin K (Cancer research 2018) 3

Products for NKX2-4 Gene

Sources for NKX2-4 Gene