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KDM8 lysine demethylase 8 [ Homo sapiens (human) ]

Gene ID: 79831, updated on 25-Nov-2021

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
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
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Genomic context

See KDM8 in Genome Data Viewer
Location:
16p12.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (27203486..27222305)
105.20201022 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 NSE1 homolog, SMC5-SMC6 complex component Neighboring gene Sharpr-MPRA regulatory region 5139 Neighboring gene NSMCE1 divergent transcript

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • FLJ13798

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 H3-methyl-lysine-36 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3-methyl-lysine-36 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 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 organization 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 histone H3-K36 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated 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
 
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 nucleoplasm IDA
Inferred from Direct Assay
more info
 
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 

General protein information

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_016879166.1
XP_016879167.1
XP_016879168.1
XP_016879169.1

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_001145348.2NP_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:233454
    Cupin_8; Cupin-like domain
  2. NM_024773.3NP_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
    Q8N371
    UniProtKB/TrEMBL
    A0A0S2Z5T1
    Related
    ENSP00000286096.5, ENST00000286096.9
    Conserved Domains (1) summary
    pfam13621
    Location:195416
    Cupin_8; Cupin-like domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    27203486..27222305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0S2Z5P8
    Conserved Domains (1) summary
    pfam13621
    Location:195385
    Cupin_8; Cupin-like domain
  2. XM_017023679.2XP_016879168.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

    Conserved Domains (1) summary
    pfam13621
    Location:1199
    Cupin_8; Cupin-like domain
  3. XM_017023677.2XP_016879166.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

    Conserved Domains (1) summary
    pfam13621
    Location:1199
    Cupin_8; Cupin-like domain
  4. XM_017023678.2XP_016879167.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

    Conserved Domains (1) summary
    pfam13621
    Location:1199
    Cupin_8; Cupin-like domain
  5. XM_017023680.1XP_016879169.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3

    Conserved Domains (1) summary
    pfam13621
    Location:1164
    Cupin_8; Cupin-like domain

RNA

  1. XR_001751987.1 RNA Sequence

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