Kdm8 lysine (K)-specific demethylase 8 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm8provided by MGI
Official Full Name: lysine (K)-specific demethylase 8provided by MGI
Primary source: MGI:MGI:1924285
See related: Ensembl:ENSMUSG00000030752 AllianceGenome:MGI:1924285
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: Jmjd5; 3110005O21Rik
Summary: Enables chromatin binding activity and p53 binding activity. Involved in circadian regulation of gene expression and protein destabilization. Acts upstream of or within several processes, including fibroblast proliferation; regulation of DNA-binding transcription factor activity; and regulation of signal transduction by p53 class mediator. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; early conceptus; genitourinary system; and trachea. Orthologous to human KDM8 (lysine demethylase 8). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 9.3), ovary adult (RPKM 7.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 F3; 7 68.85 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (125043788..125062823)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (125444620..125463651)

Chromosome 7 - NC_000073.7 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?

we report sustained Schwann cell proliferation caused by an increased expression of the direct Miz1 target gene Kdm8, encoding a H3K36me2 demethylase
Title: Miz1 Controls Schwann Cell Proliferation via H3K36(me2) Demethylase Kdm8 to Prevent Peripheral Nerve Demyelination.
The protease activities of JMJD5 and JMJD7 represent a mechanism for removal of histone tails bearing methylated arginine residues and define a potential mechanism of transcription regulation.
Title: Clipping of arginine-methylated histone tails by JMJD5 and JMJD7.
Jmjd5 is involved in the transcriptional regulation of a subset of p53-regulated genes, possibly through the control of p53 recruitment at the gene loci.
Title: Jmjd5 functions as a regulator of p53 signaling during mouse embryogenesis.
Data suggest that Jmjd5 partially accumulates on mitotic spindles during mitosis; depletion of Jmjd5 results in significant mitotic arrest, spindle assembly defects, and sustained activation of spindle assembly checkpoint.
Title: JMJD5 (Jumonji Domain-containing 5) Associates with Spindle Microtubules and Is Required for Proper Mitosis.
Collectively, these data indicate that JMJD5 is essential during embryonal development and a repressor of p53 expression. The latter suggests that JMJD5 has oncogenic activity and accordingly JMJD5 is upregulated in leukemias and breast cancer.
Title: Histone demethylase JMJD5 is essential for embryonic development.
Results suggest that Jmjd5 physiologically moderates embryonic cell proliferation through the epigenetic control of Cdkn1a expression.
Title: Jmjd5, an H3K36me2 histone demethylase, modulates embryonic cell proliferation through the regulation of Cdkn1a expression.

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Variation

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Alleles

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

Endonuclease-mediated (3)
Gene trapped (1)
Targeted (6) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables aminopeptidase activity	IEA Inferred from Electronic Annotation more info
enables aminopeptidase activity	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables p53 binding	IDA Inferred from Direct Assay more info	PubMed
enables peptidyl-arginine 3-dioxygenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables peptidyl-arginine 3-dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables peptidyl-arginine 3-dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in G2/M transition of mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fibroblast proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within fibroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of signal transduction by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: bifunctional peptidase and arginyl-hydroxylase JMJD5

Names: L-arginine (3R)-hydroxylase KDM8; arginyl C3-hydroxylase KDM8; jmjC domain-containing protein 5; jumonji C domain-containing protein 5; jumonji domain containing 5; jumonji domain-containing protein 5; lysine-specific demethylase 8

NP_084118.1

EC 1.14.11.73

XP_017167873.1

EC 1.14.11.73

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_029842.5 → NP_084118.1 bifunctional peptidase and arginyl-hydroxylase JMJD5

See identical proteins and their annotated locations for NP_084118.1

Status: VALIDATED

Source sequence(s)

AC125187, AK014006

Consensus CDS

CCDS21821.1

UniProtKB/Swiss-Prot

Q9CXT6

Related

ENSMUSP00000033010.3, ENSMUST00000033010.9

Conserved Domains (1) summary

pfam13621
Location:189 → 414

Cupin_8; Cupin-like domain

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_000073.7 Reference GRCm39 C57BL/6J

Range

125043788..125062823

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017312384.3 → XP_017167873.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X1

Conserved Domains (1) summary

pfam13621
Location:21 → 238

Cupin_8; Cupin-like domain