KDM8 lysine demethylase 8 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM8provided by HGNC
Official Full Name: lysine demethylase 8provided by HGNC
Primary source: HGNC:HGNC:25840
See related: Ensembl:ENSG00000155666 MIM:611917; AllianceGenome:HGNC:25840
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: JMJD5
Summary: This gene likely encodes a histone lysine demethylase. Studies of a similar protein in mouse indicate a potential role for this protein as a tumor suppressor. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2009]
Expression: Broad expression in liver (RPKM 13.5), small intestine (RPKM 5.4) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p12.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (27203526..27221768)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (27482139..27500381)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (27214847..27233089)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

JMJD5 inhibits lung cancer progression by facilitating EGFR proteasomal degradation.
Title: JMJD5 inhibits lung cancer progression by facilitating EGFR proteasomal degradation.
Jumonji-C domain-containing protein 5 suppresses proliferation and aerobic glycolysis in pancreatic cancer cells in a c-Myc-dependent manner.
Title: Jumonji-C domain-containing protein 5 suppresses proliferation and aerobic glycolysis in pancreatic cancer cells in a c-Myc-dependent manner.
JMJD5 couples with CDK9 to release the paused RNA polymerase II.
Title: JMJD5 couples with CDK9 to release the paused RNA polymerase II.
Downregulation of Jumonji-C domain-containing protein 5 inhibits proliferation by silibinin in the oral cancer PDTX model.
Title: Downregulation of Jumonji-C domain-containing protein 5 inhibits proliferation by silibinin in the oral cancer PDTX model.
Recognition between JMJD5/JMJD7 and histone substrates is specific, which is reflected by the binding data between enzymes and substrates. High structural similarity between JMJD5 and JMJD7 is reflected by the shared common substrates and high binding affinity.
Title: Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7.
JMJD5 expression is increased in oral squamous cell carcinoma tissue samples and tumor cell lines.
Title: Down-regulation of JMJD5 suppresses metastasis and induces apoptosis in oral squamous cell carcinoma by regulating p53/NF-κB pathway.
KDM8/JMJD5exhibits a novel property as a dual coactivator of AR and PKM2 and as such, it is a potent inducer of castration and therapy resistance.Its oncogenic properties in prostate cancer come from its direct interaction with AR to affect androgen response and with PKM2 to regulate tumor metabolism.
Title: KDM8/JMJD5 as a dual coactivator of AR and PKM2 integrates AR/EZH2 network and tumor metabolism in CRPC.
JMJD5 catalyzes stereoselective C-3 hydroxylation of arginine residues in sequences from human RCCD1 and ribosomal protein S6.
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Here, we report that JMJD5, a Jumonji C (JmjC) domain-containing protein, is a Cathepsin L-type protease that mediates histone H3 N-tail proteolytic cleavage under stress conditions that cause a DNA damage response.
Title: JMJD5 cleaves monomethylated histone H3 N-tail under DNA damaging stress.
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.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

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

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

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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

General protein information

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Preferred Names: bifunctional peptidase and arginyl-hydroxylase JMJD5

Names: JmjC arginyl-hydroxylase; 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 (K)-specific demethylase 8; lysine-specific demethylase 8

NP_001138820.1

EC 1.14.11.73

NP_079049.2

EC 1.14.11.73

XP_016879165.1

EC 1.14.11.73

XP_047290610.1

EC 1.14.11.73

XP_047290611.1

EC 1.14.11.73

XP_047290612.1

EC 1.14.11.73

XP_047290613.1

EC 1.14.11.73

XP_047290614.1

EC 1.14.11.73

XP_054169927.1

EC 1.14.11.73

XP_054169928.1

EC 1.14.11.73

XP_054169929.1

EC 1.14.11.73

XP_054169930.1

EC 1.14.11.73

XP_054169931.1

EC 1.14.11.73

XP_054169932.1

EC 1.14.11.73

XP_054169933.1

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_001145348.2 → NP_001138820.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform 1

See identical proteins and their annotated locations for NP_001138820.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC092725, AK225066, AK297166, BC027911, BQ022832

Consensus CDS

CCDS45448.1

UniProtKB/Swiss-Prot

Q8N371

Related

ENSP00000398410.2, ENST00000441782.6

Conserved Domains (1) summary

pfam13621
Location:233 → 454

Cupin_8; Cupin-like domain
NM_024773.3 → NP_079049.2 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform 2

See identical proteins and their annotated locations for NP_079049.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate 5' terminal exon and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AK225066, BC027911, BQ022832

Consensus CDS

CCDS10627.1

UniProtKB/Swiss-Prot

B4DLU9, Q6VAK5, Q8N371, Q9H8B1

UniProtKB/TrEMBL

A0A0S2Z5T1

Related

ENSP00000286096.5, ENST00000286096.9

Conserved Domains (1) summary

pfam13621
Location:195 → 416

Cupin_8; Cupin-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

27203526..27221768

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017023676.2 → XP_016879165.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X1

UniProtKB/TrEMBL

A0A0S2Z5P8

Conserved Domains (1) summary

pfam13621
Location:195 → 385

Cupin_8; Cupin-like domain
XM_047434654.1 → XP_047290610.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2
XM_047434655.1 → XP_047290611.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3
XM_047434656.1 → XP_047290612.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4
XM_047434657.1 → XP_047290613.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4
XM_047434658.1 → XP_047290614.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

UniProtKB/TrEMBL

B4DPM6

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

27482139..27500381

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054313952.1 → XP_054169927.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X1

UniProtKB/TrEMBL

A0A0S2Z5P8
XM_054313953.1 → XP_054169928.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2
XM_054313954.1 → XP_054169929.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3
XM_054313958.1 → XP_054169933.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

UniProtKB/TrEMBL

B4DPM6
XM_054313955.1 → XP_054169930.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4
XM_054313956.1 → XP_054169931.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4
XM_054313957.1 → XP_054169932.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

UniProtKB/TrEMBL

B4DPM6