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JMJD4 jumonji domain containing 4 [ Homo sapiens (human) ]

Gene ID: 65094, updated on 25-Jan-2022

Summary

Official Symbol
JMJD4provided by HGNC
Official Full Name
jumonji domain containing 4provided by HGNC
Primary source
HGNC:HGNC:25724
See related
Ensembl:ENSG00000081692 AllianceGenome:HGNC:25724
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables 2-oxoglutarate-dependent dioxygenase activity. Involved in positive regulation of translational termination and protein hydroxylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Nov 2021]
Expression
Ubiquitous expression in testis (RPKM 7.3), adrenal (RPKM 6.8) and 25 other tissues See more
Orthologs
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Genomic context

See JMJD4 in Genome Data Viewer
Location:
1q42.13
Exon count:
6
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (227731191..227735499, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (227918892..227923003, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 678 Neighboring gene vomeronasal 1 receptor 15 pseudogene Neighboring gene zinc finger protein 847, pseudogene Neighboring gene synaptosome associated protein 47 Neighboring gene LOC105373289 Neighboring gene serine protease 38

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Phenotypes

EBI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • FLJ12517, MGC129896

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3-methyl-arginine-3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables peptidyl-lysine 4-dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in histone H4-R3 demethylation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H4-R3 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of translational termination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of translational termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein hydroxylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in protein hydroxylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
2-oxoglutarate and iron-dependent oxygenase JMJD4
Names
2-oxoglutarate- and Fe(II)-dependent oxygenase
C4 lysyl hydroxylase
jmjC domain-containing protein 4
jumonji domain-containing protein 4
lysyl-hydroxylase JMJD4
NP_001154937.2
NP_075383.3
XP_011542564.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001161465.2NP_001154937.2  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter isoform (2) compared to isoform 1.
    Source sequence(s)
    AL136378
    Consensus CDS
    CCDS59203.1
    Related
    ENSP00000387830.3, ENST00000438896.3
    Conserved Domains (1) summary
    cl40423
    Location:42288
    cupin_RmlC-like; RmlC-like cupin superfamily
  2. NM_023007.3NP_075383.3  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL136378
    Consensus CDS
    CCDS1561.1
    Related
    ENSP00000477669.1, ENST00000620518.5
    Conserved Domains (1) summary
    cl40423
    Location:42288
    cupin_RmlC-like; RmlC-like cupin superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    227731191..227735499 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544262.3XP_011542564.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

    Conserved Domains (1) summary
    cl21464
    Location:88320
    cupin_like; Conserved domain found in cupin and related proteins
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