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Kdm4a lysine (K)-specific demethylase 4A [ Mus musculus (house mouse) ]

Gene ID: 230674, updated on 12-Aug-2018

Summary

Official Symbol
Kdm4aprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Aprovided by MGI
Primary source
MGI:MGI:2446210
See related
Ensembl:ENSMUSG00000033326 Vega:OTTMUSG00000008717
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Jmjd2; JHDM3A; Jmjd2a; mKIAA0677; D4Ertd222e
Expression
Ubiquitous expression in CNS E11.5 (RPKM 27.6), CNS E14 (RPKM 25.9) and 28 other tissues See more
Orthologs

Genomic context

See Kdm4a in Genome Data Viewer
Location:
4 D2.1; 4 54.31 cM
Exon count:
23
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 4 NC_000070.6 (118136957..118180043, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (117809609..117852648, complement)

Chromosome 4 - NC_000070.6Genomic Context describing neighboring genes Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3 Neighboring gene artemin Neighboring gene RIKEN cDNA 9530034E10 gene Neighboring gene microRNA 7226 Neighboring gene protein tyrosine phosphatase, receptor type, F Neighboring gene predicted gene, 40235

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC28562

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K36 specific) ISO
Inferred from Sequence Orthology
more info
 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylated histone binding ISO
Inferred from Sequence Orthology
more info
 
oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
cardiac muscle hypertrophy in response to stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
histone H3-K36 demethylation ISO
Inferred from Sequence Orthology
more info
 
histone H3-K9 demethylation ISO
Inferred from Sequence Orthology
more info
 
histone demethylation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of astrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of autophagy ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell death ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
negative regulation of histone H3-K9 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
positive regulation of neuron differentiation ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
fibrillar center ISO
Inferred from Sequence Orthology
more info
 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4A
Names
jmjC domain-containing histone demethylation protein 3A
jumonji domain containing 2A
jumonji domain-containing protein 2A
NP_001155295.1
NP_759014.2
XP_006503073.1
XP_006503074.1

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_001161823.1NP_001155295.1  lysine-specific demethylase 4A isoform 1

    See identical proteins and their annotated locations for NP_001155295.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK054095, AL626764, BY308642
    Consensus CDS
    CCDS51282.1
    UniProtKB/Swiss-Prot
    Q8BW72
    Related
    ENSMUSP00000102014.2, OTTMUSP00000009078, ENSMUST00000106406.8, OTTMUST00000019803
    Conserved Domains (5) summary
    smart00545
    Location:1355
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:9551010
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    JmjC; JmjC domain, hydroxylase
    cd15713
    Location:775884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    cl22851
    Location:667766
    PHD_SF; PHD finger superfamily
  2. NM_172382.2NP_759014.2  lysine-specific demethylase 4A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 3' terminal exon, compared to variant 1, that results in a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK054095, AL626764, BY308642
    Consensus CDS
    CCDS18545.1
    UniProtKB/Swiss-Prot
    Q8BW72
    UniProtKB/TrEMBL
    A2A8L9
    Related
    ENSMUSP00000062910.8, OTTMUSP00000009080, ENSMUST00000050288.8, OTTMUST00000019805
    Conserved Domains (5) summary
    smart00545
    Location:1355
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:899946
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    JmjC; JmjC domain, hydroxylase
    cd15713
    Location:775884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    cl22851
    Location:667766
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000070.6 Reference GRCm38.p4 C57BL/6J

    Range
    118136957..118180043 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006503010.2XP_006503073.1  lysine-specific demethylase 4A isoform X1

    See identical proteins and their annotated locations for XP_006503073.1

    UniProtKB/Swiss-Prot
    Q8BW72
    Related
    ENSMUSP00000095524.2, OTTMUSP00000009079, ENSMUST00000097911.8, OTTMUST00000019804
    Conserved Domains (5) summary
    smart00545
    Location:1355
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:9551010
    TUDOR; Tudor domain
    pfam02373
    Location:175291
    JmjC; JmjC domain, hydroxylase
    cd15713
    Location:775884
    ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
    cl22851
    Location:667766
    PHD_SF; PHD finger superfamily
  2. XM_006503011.3XP_006503074.1  lysine-specific demethylase 4A isoform X2

    Conserved Domains (2) summary
    smart00545
    Location:1355
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:175291
    JmjC; JmjC domain, hydroxylase
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