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

Gene ID: 65094, updated on 17-Jun-2024

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, Apr 2022]
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
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (227731191..227735302, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (226920125..226924236, complement)
105.20220307 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 ReSE screen-validated silencer GRCh37_chr1:227880161-227880375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:227898535-227899471 Neighboring gene zinc finger protein 847, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227915603-227916208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227928395-227928940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227928941-227929485 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227929473-227929676 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:227937705-227938206 Neighboring gene synaptosome associated protein 47 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:227949169-227949919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:227952921-227953670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227953671-227954420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227961766-227962583 Neighboring gene MPRA-validated peak747 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227965808-227966590 Neighboring gene LOC105373289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227980229-227980892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227981557-227982220 Neighboring gene MPRA-validated peak748 silencer 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

Clone Names

  • FLJ12517, MGC129896

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables 2-oxoglutarate-dependent dioxygenase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables peptidyl-lysine 4-dioxygenase activity EXP
Inferred from Experiment
more info
PubMed 
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
 
Process Evidence Code Pubs
involved_in positive regulation of translational termination IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

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_011542564.2
XP_054194371.1

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
    CCDS59203.2
    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
    CCDS1561.2
    UniProtKB/Swiss-Prot
    A0A087WT84, Q5TBZ1, Q5TBZ6, Q9H970, Q9H9V9
    Related
    ENSP00000477669.1, ENST00000620518.5
    Conserved Domains (1) summary
    cl40423
    Location:42288
    cupin_RmlC-like; RmlC-like cupin superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    227731191..227735302 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544262.4XP_011542564.2  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    226920125..226924236 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338396.1XP_054194371.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1