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KDM4D lysine demethylase 4D [ Homo sapiens (human) ]

Gene ID: 55693, updated on 6-Jan-2019

Summary

Official Symbol
KDM4Dprovided by HGNC
Official Full Name
lysine demethylase 4Dprovided by HGNC
Primary source
HGNC:HGNC:25498
See related
Ensembl:ENSG00000186280 MIM:609766
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
Also known as
JMJD2D
Expression
Biased expression in testis (RPKM 26.3) and brain (RPKM 0.6) See more
Orthologs

Genomic context

See KDM4D in Genome Data Viewer
Location:
11q21
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (94973681..94999514)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (94706845..94732678)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ST13, Hsp70 interacting protein pseudogene 11 Neighboring gene CWC15 spliceosome associated protein homolog Neighboring gene general transcription factor IIE subunit 2 pseudogene Neighboring gene lysine demethylase 4D pseudogene Neighboring gene lysine demethylase 4E

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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of lysine (K)-specific demethylase 4D (KDM4D) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10251, MGC141909

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
 
damaged DNA binding IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
blood microparticle HDA PubMed 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4D
Names
jmjC domain-containing histone demethylation protein 3D
jumonji domain containing 2D
jumonji domain-containing protein 2D
lysine (K)-specific demethylase 4D

NCBI Reference Sequences (RefSeq)

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_018039.3NP_060509.2  lysine-specific demethylase 4D

    See identical proteins and their annotated locations for NP_060509.2

    Status: VALIDATED

    Source sequence(s)
    AK056162, AP002383, AW593120, BC031862, CA311555
    Consensus CDS
    CCDS8302.1
    UniProtKB/Swiss-Prot
    Q6B0I6
    Related
    ENSP00000334181.5, ENST00000335080.5
    Conserved Domains (2) summary
    pfam02373
    Location:179295
    JmjC; JmjC domain, hydroxylase
    pfam02375
    Location:1953
    JmjN; jmjN domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    94973681..94999514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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