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

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 H3K9 demethylase activity. Acts upstream of or within DNA damage response. Located in nucleus; pericentric heterochromatin; and site of double-strand break. Orthologous to human KDM4D (lysine demethylase 4D). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward testis adult (RPKM 31.3) See more
Orthologs: human all
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Genomic context

Location:: 9 A1- A2; 9 4.05 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Kdm4d mutant mice show impaired sperm motility and subfertility.
Title: Kdm4d mutant mice show impaired sperm motility and subfertility.
Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce beta-defensin expression.
Title: Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce β-defensin expression.
Demethylase JMJD2D induces PD-L1 expression to promote colorectal cancer immune escape by enhancing IFNGR1-STAT3-IRF1 signaling.
Title: Demethylase JMJD2D induces PD-L1 expression to promote colorectal cancer immune escape by enhancing IFNGR1-STAT3-IRF1 signaling.
TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.
Title: TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.
Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling.
Title: Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling.
Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells.
Title: Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells.
To determine the epigenetic mechanisms limiting CM cycling in adult cardiac myocytes (CMs) (ACMs) and whether trimethylation of lysine 9 of histone H3 (H3K9me3), a histone modification associated with repressed chromatin, is required for the silencing of cell cycle genes, we developed a transgenic mouse model where H3K9me3 is specifically removed in CMs by overexpression of histone demethylase, KDM4D
Title: Repressive histone methylation regulates cardiac myocyte cell cycle exit.
JMJD2D interacts with b-catenin to activate transcription of its target genes and promote CRC cell proliferation, migration, and invasion, as well as formation of colorectal tumors in mice.
Title: Histone Demethylase JMJD2D Interacts With β-Catenin to Induce Transcription and Activate Colorectal Cancer Cell Proliferation and Tumor Growth in Mice.
These results suggest that demethylation of H3K9 in round spermatids is dispensable for spermatogenesis but that possible defects in Kdm4d-null elongating spermatids could be rescued by functional redundancy of the KDM4B demethylase.
Title: The testis-enriched histone demethylase, KDM4D, regulates methylation of histone H3 lysine 9 during spermatogenesis in the mouse but is dispensable for fertility.

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Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
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	IEA Inferred from Electronic Annotation 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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cellular response to ionizing radiation	ISO Inferred from Sequence Orthology more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of chromatin binding	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within positive regulation of double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
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

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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_001397435.1

EC 1.14.11.66

NP_775609.2

EC 1.14.11.66

XP_006510333.1

EC 1.14.11.66

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)

NM_001410506.1 → NP_001397435.1 lysine-specific demethylase 4D

Status: VALIDATED

Source sequence(s)

CT485607

UniProtKB/Swiss-Prot

A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19

UniProtKB/TrEMBL

Z4YLE9

Related

ENSMUSP00000111311.3, ENSMUST00000115647.3
NM_173433.3 → NP_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

A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19

UniProtKB/TrEMBL

Z4YLE9

Related

ENSMUSP00000061632.7, ENSMUST00000058796.7

Conserved Domains (2) summary

smart00545
Location:15 → 55

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

14373844..14411818 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

See identical proteins and their annotated locations for XP_006510333.1

UniProtKB/Swiss-Prot

A2CGB5, B8JK34, Q2M1G7, Q3U2K5, Q8BI19

UniProtKB/TrEMBL

Z4YLE9

Conserved Domains (2) summary

smart00545
Location:15 → 55

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase