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KDM8 lysine demethylase 8 [ Homo sapiens (human) ]

Gene ID: 79831, updated on 2-Nov-2024

Summary

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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

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See KDM8 in Genome Data Viewer
Location:
16p12.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (27203526..27221768)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (27482139..27500381)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (27214847..27233089)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371155 Neighboring gene long intergenic non-protein coding RNA 2129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:27228002-27228794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27233716-27234401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:27247181-27247705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10614 Neighboring gene Sharpr-MPRA regulatory region 5139 Neighboring gene NSE1 homolog, SMC5-SMC6 complex component Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27270255-27270754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7299 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27282975-27283523 Neighboring gene NSMCE1 divergent transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:27322486-27323685 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:27324508-27325238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7303 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:27335787-27336641 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:27338789-27339453 Neighboring gene interleukin 4 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27374892-27375392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27375393-27375893

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Identification and functional implication of nuclear localization signals in the N-terminal domain of JMJD5. Huang X, et al. Biochimie, 2013 Nov. PMID 23948433
  2. Jumonji-C domain-containing protein 5 suppresses proliferation and aerobic glycolysis in pancreatic cancer cells in a c-Myc-dependent manner. Wang H, et al. Cell Signal, 2022 May. PMID 35176452
  3. Histone lysine demethylases: emerging roles in development, physiology and disease. Shi Y. Nat Rev Genet, 2007 Nov. PMID 17909537
  4. Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function. Del Rizzo PA, et al. Mol Cell Biol, 2012 Oct. PMID 22851697, Free PMC Article
  5. JMJD5 is a potential oncogene for colon carcinogenesis. Zhang R, et al. Int J Clin Exp Pathol, 2015. PMID 26261525, Free PMC Article

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. JMJD5 inhibits lung cancer progression by facilitating EGFR proteasomal degradation.
    Title: JMJD5 inhibits lung cancer progression by facilitating EGFR proteasomal degradation.
  2. 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.
  3. JMJD5 couples with CDK9 to release the paused RNA polymerase II.
    Title: JMJD5 couples with CDK9 to release the paused RNA polymerase II.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ13798

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables aminopeptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
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
NP_079049.2
XP_016879165.1
XP_047290610.1
XP_047290611.1
XP_047290612.1
XP_047290613.1
XP_047290614.1
XP_054169927.1
XP_054169928.1
XP_054169929.1
XP_054169930.1
XP_054169931.1
XP_054169932.1
XP_054169933.1

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)

  1. 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

  2. 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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    27203526..27221768
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_047434654.1 → XP_047290610.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

  3. XM_047434655.1 → XP_047290611.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3

  4. XM_047434656.1 → XP_047290612.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4

  5. XM_047434657.1 → XP_047290613.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4

  6. XM_047434658.1 → XP_047290614.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    27482139..27500381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0S2Z5P8

  2. XM_054313953.1 → XP_054169928.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

  3. XM_054313954.1 → XP_054169929.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3

  4. XM_054313958.1 → XP_054169933.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

  5. XM_054313955.1 → XP_054169930.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4

  6. XM_054313956.1 → XP_054169931.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4

  7. XM_054313957.1 → XP_054169932.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N371.1 GenPept UniProtKB/Swiss-Prot:Q8N371

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