U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Kdm4d lysine (K)-specific demethylase 4D [ Mus musculus (house mouse) ]

Gene ID: 244694, updated on 8-Dec-2022

Summary

Official Symbol
Kdm4dprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Dprovided by MGI
Primary source
MGI:MGI:3606484
See related
Ensembl:ENSMUSG00000053914 AllianceGenome:MGI:3606484
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
Jmjd2d; 4932416A15
Summary
Enables chromatin DNA binding activity; damaged DNA binding activity; and histone H3-methyl-lysine-9 demethylase activity. Acts upstream of or within cellular response to DNA damage stimulus; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in nucleus; pericentric heterochromatin; and site of double-strand break. Orthologous to several human genes including KDM4D (lysine demethylase 4D). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis adult (RPKM 31.3) See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Kdm4d in Genome Data Viewer
Location:
9; 9 A1- A2
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (14373844..14411818, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (14462548..14500522, complement)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene endonuclease domain containing 1 Neighboring gene predicted gene, 34156 Neighboring gene lysine (K)-specific demethylase 4D-like Neighboring gene CWC15 spliceosome-associated protein Neighboring gene angiomotin-like 1 Neighboring gene predicted gene, 34263

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 Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K9 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4D
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4D
jmjC domain-containing histone demethylation protein 3D
jumonji domain containing 2D
jumonji domain-containing protein 2D
NP_775609.2
XP_006510333.1
XP_006510334.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001410506.1NP_001397435.1  lysine-specific demethylase 4D

    Status: VALIDATED

    Source sequence(s)
    CT485607
    UniProtKB/Swiss-Prot
    Q8BI19
  2. NM_173433.3NP_775609.2  lysine-specific demethylase 4D

    See identical proteins and their annotated locations for NP_775609.2

    Status: VALIDATED

    Source sequence(s)
    CT485607
    Consensus CDS
    CCDS22822.2
    UniProtKB/Swiss-Prot
    Q3U2K5, Q8BI19
    Related
    ENSMUSP00000061632.7, ENSMUST00000058796.7
    Conserved Domains (2) summary
    smart00545
    Location:1555
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    14373844..14411818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006510270.2XP_006510333.1  lysine-specific demethylase 4D isoform X1

    See identical proteins and their annotated locations for XP_006510333.1

    UniProtKB/Swiss-Prot
    Q3U2K5, Q8BI19
    Conserved Domains (2) summary
    smart00545
    Location:1555
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  2. XM_006510271.2XP_006510334.1  lysine-specific demethylase 4D isoform X1

    UniProtKB/Swiss-Prot
    Q3U2K5
    Related
    ENSMUSP00000111311.3, ENSMUST00000115647.3
    Conserved Domains (2) summary
    smart00545
    Location:1555
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase