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Aliases for KDM8 Gene

Aliases for KDM8 Gene

  • Lysine Demethylase 8 2 3 5
  • Jumonji Domain-Containing Protein 5 3 4
  • Lysine (K)-Specific Demethylase 8 2 3
  • Lysine-Specific Demethylase 8 3 4
  • Jumonji Domain Containing 5 2 3
  • JMJD5 3 4
  • JmjC Domain-Containing Protein 5 3
  • EC 1.14.11.27 4
  • EC 3.4.-.- 4

External Ids for KDM8 Gene

Previous HGNC Symbols for KDM8 Gene

  • JMJD5

Summaries for KDM8 Gene

Entrez Gene Summary for KDM8 Gene

  • 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]

GeneCards Summary for KDM8 Gene

KDM8 (Lysine Demethylase 8) is a Protein Coding gene. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include chromatin binding and histone demethylase activity (H3-K36 specific). An important paralog of this gene is HIF1AN.

UniProtKB/Swiss-Prot for KDM8 Gene

  • Histone demethylase required for G2/M phase cell cycle progression (PubMed:20457893). Specifically demethylates dimethylated Lys-36 (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator (PubMed:20457893). Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation (PubMed:20457893). In a complex with coregulator RCCD1, is also able to demethylate trimethylated Lys-36 (H3K36me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with RCCD1 (PubMed:24981860). Possibly together with RCCD1, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin acetylation and cytoskeletal microtubule stability (PubMed:28455245). Might function as a protein hydroxylase (PubMed:22851697, PubMed:24100311). Under stress conditions that cause a DNA damage response, acts as a histone protease by cleaving the N-terminal tail of histone H3 at the carboxyl side of monomethyl-lysine (Kme1) residues, preferably at monomethylated Lys-9 (H3K9me1) (PubMed:28982940). The histone variant H3F3A is the major target for cleavage (PubMed:28982940).

Additional gene information for KDM8 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM8 Gene

Genomics for KDM8 Gene

GeneHancer (GH) Regulatory Elements for KDM8 Gene

Promoters and enhancers for KDM8 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I027202 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 557.5 +0.5 507 2.2 HDGF FOXA2 PKNOX1 CLOCK SMAD1 MLX ARNT ZFP64 ARID4B SIN3A KDM8 ENSG00000259940
GH16I027221 Enhancer 1 Ensembl ENCODE dbSUPER 21.3 +21.0 20981 6.5 CTCF ZIC2 RAD21 ATF2 NR2F2 YY1 ZNF121 POLR2A GLIS1 HNF4G KDM8 ENSG00000259940 NSMCE1 FLJ21408
GH16I027267 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.4 +65.4 65416 3.1 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B IRF4 NSMCE1 FLJ21408 IL4R KDM8 ENSG00000259940
GH16I027228 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 7.8 +34.8 34770 19.1 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 ZNF2 IRF4 ENSG00000259940 KDM8 NSMCE1 IL4R IL21R KIAA0556 FLJ21408
GH16I027429 Enhancer 1.1 ENCODE dbSUPER 11.7 +228.2 228150 3.3 PKNOX1 ARNT IRF4 GTF3C2 TCF12 GATA2 ZNF143 FOS ATF7 RUNX3 IL21R KDM8 IL21R-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KDM8 on UCSC Golden Path with GeneCards custom track

Genomic Locations for KDM8 Gene

Genomic Locations for KDM8 Gene
chr16:27,203,486-27,222,305
(GRCh38/hg38)
Size:
18,820 bases
Orientation:
Plus strand
chr16:27,214,807-27,233,089
(GRCh37/hg19)

Genomic View for KDM8 Gene

Genes around KDM8 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM8 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM8 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM8 Gene

Proteins for KDM8 Gene

  • Protein details for KDM8 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N371-KDM8_HUMAN
    Recommended name:
    JmjC domain-containing protein 5
    Protein Accession:
    Q8N371
    Secondary Accessions:
    • B4DLU9
    • Q6VAK5
    • Q9H8B1

    Protein attributes for KDM8 Gene

    Size:
    416 amino acids
    Molecular mass:
    47270 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Can form homodimers (via JmjC domain) (PubMed:24100311, PubMed:28982940). Found in a complex with RCCD1 (PubMed:24981860). Interacts (via N-terminus) with RCCD1 (via N-terminus); this interaction stimulates H3K36me3 and H3K36me2 demethylation (PubMed:24981860, PubMed:28455245). Interacts (via JmjC domain) with HIST1H3A (PubMed:28982940).

    Three dimensional structures from OCA and Proteopedia for KDM8 Gene

    Alternative splice isoforms for KDM8 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM8 Gene

Post-translational modifications for KDM8 Gene

No Post-translational modifications

No data available for DME Specific Peptides for KDM8 Gene

Domains & Families for KDM8 Gene

Gene Families for KDM8 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for KDM8 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for KDM8 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with KDM8: view

No data available for UniProtKB/Swiss-Prot for KDM8 Gene

Function for KDM8 Gene

Molecular function for KDM8 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Protein N(6),N(6)-dimethyl-L-lysine + 2 2-oxoglutarate + 2 O(2) = protein L-lysine + 2 succinate + 2 formaldehyde + 2 CO(2).
UniProtKB/Swiss-Prot Function:
Histone demethylase required for G2/M phase cell cycle progression (PubMed:20457893). Specifically demethylates dimethylated Lys-36 (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator (PubMed:20457893). Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation (PubMed:20457893). In a complex with coregulator RCCD1, is also able to demethylate trimethylated Lys-36 (H3K36me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with RCCD1 (PubMed:24981860). Possibly together with RCCD1, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin acetylation and cytoskeletal microtubule stability (PubMed:28455245). Might function as a protein hydroxylase (PubMed:22851697, PubMed:24100311). Under stress conditions that cause a DNA damage response, acts as a histone protease by cleaving the N-terminal tail of histone H3 at the carboxyl side of monomethyl-lysine (Kme1) residues, preferably at monomethylated Lys-9 (H3K9me1) (PubMed:28982940). The histone variant H3F3A is the major target for cleavage (PubMed:28982940).
UniProtKB/Swiss-Prot Induction:
Up-regulated upon starvation, DNA replication stress, UV treatment and by camptothecin and etoposide treatment.

Enzyme Numbers (IUBMB) for KDM8 Gene

Phenotypes From GWAS Catalog for KDM8 Gene

Gene Ontology (GO) - Molecular Function for KDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 20457893
GO:0008233 peptidase activity IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0032452 histone demethylase activity TAS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with KDM8: view
genes like me logo Genes that share phenotypes with KDM8: view

Animal Models for KDM8 Gene

MGI Knock Outs for KDM8:
  • Kdm8 tm1a(EUCOMM)Wtsi
  • Kdm8 tm1.2Tasu
  • Kdm8 tm1b(EUCOMM)Wtsi

Animal Model Products

miRNA for KDM8 Gene

miRTarBase miRNAs that target KDM8

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM8 Gene

Localization for KDM8 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM8 Gene

Nucleus. Chromosome. Note=Colocalizes with trimethylated Lys-9 of histone H3 (H3K9me3). {ECO:0000269 PubMed:24981860}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM8 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 20457893
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with KDM8: view

Pathways & Interactions for KDM8 Gene

genes like me logo Genes that share pathways with KDM8: view

Pathways by source for KDM8 Gene

Gene Ontology (GO) - Biological Process for KDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle IMP 20457893
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006508 proteolysis IEA --
GO:0007049 cell cycle IEA --
genes like me logo Genes that share ontologies with KDM8: view

No data available for SIGNOR curated interactions for KDM8 Gene

Drugs & Compounds for KDM8 Gene

(3) Drugs for KDM8 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Formaldehyde Approved, Vet_approved Pharma 102
Oxygen Approved, Vet_approved Pharma 0
Succinic acid Approved Nutra Full agonist, Agonist 0

(1) Additional Compounds for KDM8 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with KDM8: view

Transcripts for KDM8 Gene

Unigene Clusters for KDM8 Gene

Lysine (K)-specific demethylase 8:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM8 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b · 13c ·
SP1: -
SP2: - - -
SP3: - - -
SP4: - - -
SP5: - - - - -
SP6:
SP7: - -
SP8: -
SP9: - - - - - - -
SP10: - - - - - - - - - - - -

ExUns: 13d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for KDM8 Gene

GeneLoc Exon Structure for
KDM8
ECgene alternative splicing isoforms for
KDM8

Expression for KDM8 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM8 Gene

mRNA differential expression in normal tissues according to GTEx for KDM8 Gene

This gene is overexpressed in Liver (x15.6).

Protein differential expression in normal tissues from HIPED for KDM8 Gene

This gene is overexpressed in Blymphocyte (62.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KDM8 Gene



NURSA nuclear receptor signaling pathways regulating expression of KDM8 Gene:

KDM8

SOURCE GeneReport for Unigene cluster for KDM8 Gene:

Hs.145717

mRNA Expression by UniProt/SwissProt for KDM8 Gene:

Q8N371-KDM8_HUMAN
Tissue specificity: Weakly expressed in most cells. Highly expressed in breast cancer cells.

Evidence on tissue expression from TISSUES for KDM8 Gene

  • Nervous system(4.4)
  • Lung(4.1)
  • Thyroid gland(4.1)
genes like me logo Genes that share expression patterns with KDM8: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM8 Gene

Orthologs for KDM8 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDM8 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia JMJD5 33
  • 99.34 (n)
KDM8 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM8 33 34
  • 83.45 (n)
cow
(Bos Taurus)
Mammalia KDM8 33 34
  • 83.37 (n)
rat
(Rattus norvegicus)
Mammalia Kdm8 33
  • 79.42 (n)
mouse
(Mus musculus)
Mammalia Kdm8 33 16 34
  • 79.18 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM8 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM8 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM8 33 34
  • 66.33 (n)
lizard
(Anolis carolinensis)
Reptilia KDM8 34
  • 54 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm8 33
  • 61.68 (n)
zebrafish
(Danio rerio)
Actinopterygii kdm8 33 34
  • 59.93 (n)
Dr.16868 33
fruit fly
(Drosophila melanogaster)
Insecta CG13902 33 34
  • 52.35 (n)
worm
(Caenorhabditis elegans)
Secernentea jmjd-5 33 34
  • 46.34 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G20810 33
  • 49.47 (n)
soybean
(Glycine max)
eudicotyledons Gma.17248 33
rice
(Oryza sativa)
Liliopsida Os09g0489200 33
  • 52.22 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.15579 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.718 34
  • 17 (a)
ManyToMany
Species where no ortholog for KDM8 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for KDM8 Gene

ENSEMBL:
Gene Tree for KDM8 (if available)
TreeFam:
Gene Tree for KDM8 (if available)

Paralogs for KDM8 Gene

Paralogs for KDM8 Gene

genes like me logo Genes that share paralogs with KDM8: view

Variants for KDM8 Gene

Sequence variations from dbSNP and Humsavar for KDM8 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000047656 -- 27,205,426(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000129015 -- 27,206,737(+) T/A genic_upstream_transcript_variant, intron_variant
rs1000315616 -- 27,216,787(+) C/T intron_variant
rs1000379513 -- 27,217,854(+) A/G intron_variant
rs1000435873 -- 27,201,747(+) G/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for KDM8 Gene

Variant ID Type Subtype PubMed ID
dgv2828n100 CNV gain 25217958
esv3638319 CNV gain 21293372
nsv1059454 CNV gain 25217958
nsv952959 CNV deletion 24416366

Variation tolerance for KDM8 Gene

Residual Variation Intolerance Score: 51.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.56; 30.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM8 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM8

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM8 Gene

Disorders for KDM8 Gene

Additional Disease Information for KDM8

No disorders were found for KDM8 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM8 Gene

Publications for KDM8 Gene

  1. KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation. (PMID: 20457893) Hsia DA … Izumiya Y (Proceedings of the National Academy of Sciences of the United States of America 2010) 2 3 4 58
  2. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. (PMID: 24981860) Marcon E … Greenblatt J (Cell reports 2014) 3 4 58
  3. Structure of the JmjC-domain-containing protein JMJD5. (PMID: 24100311) Wang H … Zang J (Acta crystallographica. Section D, Biological crystallography 2013) 3 4 58
  4. Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function. (PMID: 22851697) Del Rizzo PA … Trievel RC (Molecular and cellular biology 2012) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for KDM8 Gene

  • Addgene plasmids for KDM8

Sources for KDM8 Gene

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