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Aliases for KDM5D Gene

Aliases for KDM5D Gene

  • Lysine Demethylase 5D 2 3 5
  • Jumonji, AT Rich Interactive Domain 1D (RBP2-Like) 2 3
  • Jumonji/ARID Domain-Containing Protein 1D 3 4
  • Lysine (K)-Specific Demethylase 5D 2 3
  • Histocompatibility Y Antigen 3 4
  • Histone Demethylase JARID1D 3 4
  • Protein SmcY 3 4
  • JARID1D 3 4
  • SMCY 3 4
  • HYA 3 4
  • H-Y 3 4
  • HY 3 4
  • Selected Mouse CDNA On Y, Human Homolog Of 3
  • Jumonji, AT Rich Interactive Domain 1D 2
  • Smcy Homolog, Y-Linked (Mouse) 2
  • Lysine-Specific Demethylase 5D 3
  • SMC Homolog, Y Chromosome 3
  • Smcy Homolog, Y-Linked 3
  • EC 1.14.11.- 4
  • EC 1.14.11 61
  • KIAA0234 4

External Ids for KDM5D Gene

Previous HGNC Symbols for KDM5D Gene

  • HYA
  • HY
  • SMCY
  • JARID1D

Previous GeneCards Identifiers for KDM5D Gene

  • GC0YM020326
  • GC0YM021865
  • GC0YM015577

Summaries for KDM5D Gene

Entrez Gene Summary for KDM5D Gene

  • This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

GeneCards Summary for KDM5D Gene

KDM5D (Lysine Demethylase 5D) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. GO annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors and histone demethylase activity (H3-K4 specific). An important paralog of this gene is KDM5C.

UniProtKB/Swiss-Prot for KDM5D Gene

  • Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks.

Gene Wiki entry for KDM5D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM5D Gene

Genomics for KDM5D Gene

Regulatory Elements for KDM5D Gene

Enhancers for KDM5D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0YG019502 0.3 FANTOM5 7.1 +242.6 242605 0.2 KDM5D BCORP1 LOC102723934
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM5D on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM5D Gene

Chromosome:
Y
Start:
19,703,865 bp from pter
End:
19,744,939 bp from pter
Size:
41,075 bases
Orientation:
Minus strand

Genomic View for KDM5D Gene

Genes around KDM5D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM5D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM5D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM5D Gene

Proteins for KDM5D Gene

  • Protein details for KDM5D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BY66-KDM5D_HUMAN
    Recommended name:
    Lysine-specific demethylase 5D
    Protein Accession:
    Q9BY66
    Secondary Accessions:
    • A2RU19
    • A6H8V7
    • B7ZLX1
    • Q92509
    • Q92809
    • Q9HCU1

    Protein attributes for KDM5D Gene

    Size:
    1539 amino acids
    Molecular mass:
    174073 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Interacts with PCGF6, MSH5, ZMYND8, AR.
    Miscellaneous:
    • Involved in sensitivity to docetaxel.
    SequenceCaution:
    • Sequence=BAA13241.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM5D Gene

    Alternative splice isoforms for KDM5D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM5D Gene

Selected DME Specific Peptides for KDM5D Gene

Q9BY66:
  • EAFGFEQA
  • EEGGYEAICKDRRWARVAQRL
  • NFAEAVNF
  • QRLNELEA
  • GPKMMGLGLMAKDK
  • GRQCIEHYR
  • DKEYKPH
  • RRAKRLQPDPEPTEEDIEK
  • DYFNMPVHMVPTE
  • STKRSRW
  • AVHKEMFIMVQEERRLRK
  • IVAFKEGEQKEKEGILQLRRTNSAKPSPLA
  • LMMEGDLLEV
  • LLEVLCP
  • FELLPDDERQC
  • LVAVGRDLPV
  • TFLKKNS
  • QGSSLKIP
  • MNPNTLM
  • GWNLNVMPVL
  • RTNQCAGEFV
  • LVCLSHINDLCKCS
  • CVFSHEELI
  • DTELLGLSAQDLRDPGS
  • LDQIAKFW
  • ALEVEDGRKRS
  • LEQVEAYQ
  • FLPPPECPVFEP
  • EKEFWRLV
  • RPRLETIL
  • HINADISGM
  • CLEARQKHPPATLEAII
  • EELRALESEAR
  • DPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNF
  • HYRRLRR
  • VERKILDL
  • KVQGLLENGDSV
  • CSRGDEDDKLL
  • DNYHIFCLLPPL
  • PELKKLQIYG
  • RYCVFSH
  • GEPKTWY
  • LRYRYTLD
  • KCKTTCF
  • DWFHGQCV
  • ERWEEKA
  • GKNIGSLLRSHYERI
  • EDVTVEYGAD
  • YSINYLH
  • QVLTAHSW
  • PELFDSQPDLLHQLVT
  • TTCFLSA
  • PPPECPVFEPSW
  • PWLYVGM

Post-translational modifications for KDM5D Gene

  • Ubiquitination at isoforms=2, 3752 and isoforms=2, 31281
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for KDM5D

Domains & Families for KDM5D Gene

Suggested Antigen Peptide Sequences for KDM5D Gene

Graphical View of Domain Structure for InterPro Entry

Q9BY66

UniProtKB/Swiss-Prot:

KDM5D_HUMAN :
  • The JmjC domain is required for enzymatic activity.
  • Belongs to the JARID1 histone demethylase family.
Domain:
  • The JmjC domain is required for enzymatic activity.
Family:
  • Belongs to the JARID1 histone demethylase family.
genes like me logo Genes that share domains with KDM5D: view

Function for KDM5D Gene

Molecular function for KDM5D Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks.

Enzyme Numbers (IUBMB) for KDM5D Gene

Gene Ontology (GO) - Molecular Function for KDM5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA --
GO:0032452 histone demethylase activity TAS --
genes like me logo Genes that share ontologies with KDM5D: view
genes like me logo Genes that share phenotypes with KDM5D: view

Human Phenotype Ontology for KDM5D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for KDM5D Gene

miRTarBase miRNAs that target KDM5D

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for KDM5D Gene

Localization for KDM5D Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM5D Gene

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 KDM5D gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for KDM5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM5D: view

Pathways & Interactions for KDM5D Gene

genes like me logo Genes that share pathways with KDM5D: view

Pathways by source for KDM5D Gene

1 GeneTex pathway for KDM5D Gene

Gene Ontology (GO) - Biological Process for KDM5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002457 T cell antigen processing and presentation IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0034720 histone H3-K4 demethylation IDA 17320160
genes like me logo Genes that share ontologies with KDM5D: view

No data available for SIGNOR curated interactions for KDM5D Gene

Drugs & Compounds for KDM5D Gene

(1) Drugs for KDM5D Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target 531,531
genes like me logo Genes that share compounds with KDM5D: view

Transcripts for KDM5D Gene

Unigene Clusters for KDM5D Gene

Lysine (K)-specific demethylase 5D:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM5D Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a ·
SP1: - - -
SP2: - - - -
SP3: -
SP4: - -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10:

ExUns: 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26a · 26b · 26c ^ 27 ^ 28a · 28b ^ 29a · 29b
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5: -
SP6: -
SP7: -
SP8:
SP9:
SP10: -

Relevant External Links for KDM5D Gene

GeneLoc Exon Structure for
KDM5D
ECgene alternative splicing isoforms for
KDM5D

Expression for KDM5D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM5D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KDM5D Gene

This gene is overexpressed in Serum (59.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KDM5D Gene



Protein tissue co-expression partners for KDM5D Gene

NURSA nuclear receptor signaling pathways regulating expression of KDM5D Gene:

KDM5D

SOURCE GeneReport for Unigene cluster for KDM5D Gene:

Hs.80358

mRNA Expression by UniProt/SwissProt for KDM5D Gene:

Q9BY66-KDM5D_HUMAN
Tissue specificity: Expression is highly down-regulated in metastatic prostate tumors.

Evidence on tissue expression from TISSUES for KDM5D Gene

  • Blood(4.4)
  • Bone marrow(4.4)
  • Nervous system(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM5D Gene

Germ Layers:
  • mesoderm
Systems:
  • immune
Organs:
General:
  • blood
  • white blood cell
genes like me logo Genes that share expression patterns with KDM5D: view

Primer Products

No data available for mRNA differential expression in normal tissues for KDM5D Gene

Orthologs for KDM5D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM5D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM5D 34 35
  • 99.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 81 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Kdm5d 34 16 35
  • 80.33 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 73 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 74 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii kdm5c 35
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta lid 35
  • 34 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rbr-2 35
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 35 37
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 41 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9938 34
Species where no ortholog for KDM5D 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for KDM5D Gene

ENSEMBL:
Gene Tree for KDM5D (if available)
TreeFam:
Gene Tree for KDM5D (if available)

Paralogs for KDM5D Gene

Paralogs for KDM5D Gene

Pseudogenes.org Pseudogenes for KDM5D Gene

genes like me logo Genes that share paralogs with KDM5D: view

Variants for KDM5D Gene

Sequence variations from dbSNP and Humsavar for KDM5D Gene

SNP ID Clin Chr 0Y pos Sequence Context AA Info Type
rs1000254591 -- 19,698,448(+) AAGCT(C/G)GAAGT nc-transcript-variant, utr-variant-3-prime
rs1000461704 -- 19,726,565(+) GGGGG(A/T)CTAGG intron-variant
rs1000690171 -- 19,697,198(+) GCTCA(C/T)TGTAA nc-transcript-variant, utr-variant-3-prime
rs1000731402 -- 19,721,411(+) TTAGA(A/G)CATGC intron-variant
rs1000803276 -- 19,719,743(+) TAGTC(A/G)AACCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM5D Gene

Variant ID Type Subtype PubMed ID
nsv10025 CNV gain 18304495

Variation tolerance for KDM5D Gene

Gene Damage Index Score: 1.20; 24.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM5D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM5D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM5D Gene

Disorders for KDM5D Gene

Relevant External Links for KDM5D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM5D

No disorders were found for KDM5D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM5D Gene

Publications for KDM5D Gene

  1. Gene sequence and evolutionary conservation of human SMCY. (PMID: 8841177) Kent-First M.G. … Vandeberg J. (Nat. Genet. 1996) 2 3 4 64
  2. JARID1D is a suppressor and prognostic marker of prostate cancer invasion and metastasis. (PMID: 26747897) Li N. … Lee M.G. (Cancer Res. 2016) 3 4 64
  3. Resistance to docetaxel in prostate cancer is associated with androgen receptor activation and loss of KDM5D expression. (PMID: 27185910) Komura K. … Sweeney C.J. (Proc. Natl. Acad. Sci. U.S.A. 2016) 3 4 64
  4. Spermatogenesis-specific association of SMCY and MSH5. (PMID: 18459961) Akimoto C. … Kato S. (Genes Cells 2008) 3 4 64
  5. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. (PMID: 17320160) Iwase S. … Shi Y. (Cell 2007) 3 4 64

Products for KDM5D Gene

Sources for KDM5D Gene

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