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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)

    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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    NEW Try the new Transcript table

    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

    Gene LinkOut

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