Aliases for JMJD4 Gene

Aliases for JMJD4 Gene

  • Jumonji Domain Containing 4 2 3 5
  • 2-Oxoglutarate And Iron-Dependent Oxygenase JMJD4 3 4
  • 2-Oxoglutarate- And Fe(II)-Dependent Oxygenase 2 3
  • Jumonji Domain-Containing Protein 4 3 4
  • JmjC Domain-Containing Protein 4 3 4
  • Lysyl-Hydroxylase JMJD4 3 4
  • C4 Lysyl Hydroxylase 2 3
  • EC 1.14.11.- 4
  • FLJ12517 2
  • JMJD4 5

External Ids for JMJD4 Gene

Previous GeneCards Identifiers for JMJD4 Gene

  • GC01M224226
  • GC01M225985
  • GC01M227918
  • GC01M198436

Summaries for JMJD4 Gene

GeneCards Summary for JMJD4 Gene

JMJD4 (Jumonji Domain Containing 4) is a Protein Coding gene. Diseases associated with JMJD4 include Intracranial Chondrosarcoma and Familial Isolated Hypoparathyroidism. An important paralog of this gene is JMJD6.

UniProtKB/Swiss-Prot Summary for JMJD4 Gene

  • Catalyzes the 2-oxoglutarate and iron-dependent C4-lysyl hydroxylation of ETF1 at 'Lys-63' thereby promoting the translational termination efficiency of ETF1.

Additional gene information for JMJD4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for JMJD4 Gene

Genomics for JMJD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for JMJD4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around JMJD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for JMJD4

Top Transcription factor binding sites by QIAGEN in the JMJD4 gene promoter:
  • AML1a
  • AREB6
  • ATF6
  • CUTL1
  • LUN-1
  • POU2F1
  • POU2F1a
  • STAT1

Genomic Locations for JMJD4 Gene

Genomic Locations for JMJD4 Gene
chr1:227,730,425-227,735,499
(GRCh38/hg38)
Size:
5,075 bases
Orientation:
Minus strand
chr1:227,918,126-227,923,112
(GRCh37/hg19)
Size:
4,987 bases
Orientation:
Minus strand

Genomic View for JMJD4 Gene

Genes around JMJD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
JMJD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for JMJD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for JMJD4 Gene

Proteins for JMJD4 Gene

  • Protein details for JMJD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9V9-JMJD4_HUMAN
    Recommended name:
    2-oxoglutarate and iron-dependent oxygenase JMJD4
    Protein Accession:
    Q9H9V9
    Secondary Accessions:
    • Q5TBZ1
    • Q5TBZ6
    • Q9H970

    Protein attributes for JMJD4 Gene

    Size:
    463 amino acids
    Molecular mass:
    52493 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with ETF1 (PubMed:24486019). Interacts with the ETF1-GSPT1 complex (PubMed:24486019).
    SequenceCaution:
    • Sequence=BAB14366.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for JMJD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for JMJD4 Gene

Post-translational modifications for JMJD4 Gene

  • Ubiquitination at Lys153 and Lys447
  • Modification sites at PhosphoSitePlus

Other Protein References for JMJD4 Gene

Antibody Products

  • Abcam antibodies for JMJD4
  • Santa Cruz Biotechnology (SCBT) Antibodies for JMJD4

No data available for DME Specific Peptides for JMJD4 Gene

Domains & Families for JMJD4 Gene

Gene Families for JMJD4 Gene

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

Protein Domains for JMJD4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for JMJD4 Gene

GenScript: Design optimal peptide antigens:
  • Jumonji domain-containing protein 4 (JMJD4_HUMAN)
genes like me logo Genes that share domains with JMJD4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for JMJD4 Gene

Function for JMJD4 Gene

Molecular function for JMJD4 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the 2-oxoglutarate and iron-dependent C4-lysyl hydroxylation of ETF1 at 'Lys-63' thereby promoting the translational termination efficiency of ETF1.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-oxoglutarate + L-lysyl-[protein] + O2 = 4-hydroxy-L-lysyl-[protein] + CO2 + succinate; Xref=Rhea:RHEA:57156, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:15084, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031, ChEBI:CHEBI:141495; Evidence={ECO:0000269|PubMed:24486019};.

Enzyme Numbers (IUBMB) for JMJD4 Gene

Phenotypes From GWAS Catalog for JMJD4 Gene

Gene Ontology (GO) - Molecular Function for JMJD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24360279
GO:0016491 oxidoreductase activity IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IMP 24486019
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
genes like me logo Genes that share ontologies with JMJD4: view
genes like me logo Genes that share phenotypes with JMJD4: view

Animal Models for JMJD4 Gene

MGI Knock Outs for JMJD4:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JMJD4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for JMJD4 Gene

Localization for JMJD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for JMJD4 Gene

Cytoplasm.

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 JMJD4 gene
Compartment Confidence
plasma membrane 2
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for JMJD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 24486019
genes like me logo Genes that share ontologies with JMJD4: view

Pathways & Interactions for JMJD4 Gene

PathCards logo

SuperPathways for JMJD4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for JMJD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018126 protein hydroxylation IMP 24486019
GO:0045905 positive regulation of translational termination IMP 24486019
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with JMJD4: view

No data available for Pathways by source and SIGNOR curated interactions for JMJD4 Gene

Drugs & Compounds for JMJD4 Gene

No Compound Related Data Available

Transcripts for JMJD4 Gene

mRNA/cDNA for JMJD4 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JMJD4

Alternative Splicing Database (ASD) splice patterns (SP) for JMJD4 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c
SP1: -
SP2: - -
SP3:
SP4:

Relevant External Links for JMJD4 Gene

GeneLoc Exon Structure for
JMJD4

Expression for JMJD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for JMJD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for JMJD4 Gene

This gene is overexpressed in Testis (48.8) and CD8 Tcells (20.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for JMJD4 Gene



Protein tissue co-expression partners for JMJD4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for JMJD4

SOURCE GeneReport for Unigene cluster for JMJD4 Gene:

Hs.555974

Evidence on tissue expression from TISSUES for JMJD4 Gene

  • Nervous system(4.5)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with JMJD4: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for JMJD4 Gene

Orthologs for JMJD4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for JMJD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia JMJD4 30 31
  • 99.28 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia JMJD4 30 31
  • 79.33 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Jmjd4 30
  • 79.01 (n)
Dog
(Canis familiaris)
Mammalia JMJD4 30 31
  • 78.65 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Jmjd4 30 17 31
  • 78.21 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia JMJD4 31
  • 58 (a)
OneToOne
Chicken
(Gallus gallus)
Aves JMJD4 30 31
  • 64.81 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia JMJD4 31
  • 58 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia jmjd4 30
  • 62 (n)
Zebrafish
(Danio rerio)
Actinopterygii jmjd4 30 31
  • 61.1 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008415 30
  • 53.66 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG7200 30 31
  • 50.38 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea jmjd-4 31
  • 30 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G63080 30
  • 46.49 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0546900 30
  • 48.14 (n)
Species where no ortholog for JMJD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for JMJD4 Gene

ENSEMBL:
Gene Tree for JMJD4 (if available)
TreeFam:
Gene Tree for JMJD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for JMJD4: view image

Paralogs for JMJD4 Gene

Paralogs for JMJD4 Gene

Pseudogenes.org Pseudogenes for JMJD4 Gene

genes like me logo Genes that share paralogs with JMJD4: view

Variants for JMJD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for JMJD4 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
778255 Benign: not provided 227,733,552(-) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
rs2295994 - p.Asp65Glu
rs3087908 - p.Ala461Val
rs34560898 - p.Gly16Cys
rs7419238 - p.Ala11Val

Additional dbSNP identifiers (rs#s) for JMJD4 Gene

Structural Variations from Database of Genomic Variants (DGV) for JMJD4 Gene

Variant ID Type Subtype PubMed ID
esv32853 CNV gain 17666407
nsv1007479 CNV gain 25217958
nsv515496 CNV loss 19592680
nsv826908 CNV gain 20364138

Variation tolerance for JMJD4 Gene

Residual Variation Intolerance Score: 66.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.50; 77.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for JMJD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
JMJD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for JMJD4 Gene

Disorders for JMJD4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for JMJD4 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search JMJD4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with JMJD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for JMJD4 Gene

Publications for JMJD4 Gene

  1. Optimal translational termination requires C4 lysyl hydroxylation of eRF1. (PMID: 24486019) Feng T … Coleman ML (Molecular cell 2014) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Correlation between high expression levels of jumonji domain-containing 4 and short survival in cases of colon adenocarcinoma. (PMID: 30029884) Ho YJ … Lu JW (Biochemical and biophysical research communications 2018) 3
  4. A Human Tyrosine Phosphatase Interactome Mapped by Proteomic Profiling. (PMID: 28675297) Kumar P … Maddika S (Journal of proteome research 2017) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for JMJD4 Gene

Sources for JMJD4 Gene