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Aliases for KDM5D Gene

Aliases for KDM5D Gene

  • Lysine (K)-Specific Demethylase 5D 2 3
  • JARID1D 3 4 6
  • SMCY 3 4 6
  • HYA 3 4 6
  • Jumonji, AT Rich Interactive Domain 1D (RBP2-Like) 2 3
  • Jumonji/ARID Domain-Containing Protein 1D 3 4
  • Histocompatibility Y Antigen 3 4
  • Histone Demethylase JARID1D 3 4
  • Protein SmcY 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 64
  • KIAA0234 4

External Ids for KDM5D Gene

Previous Symbols for KDM5D Gene

  • HYA
  • HY
  • SMCY
  • JARID1D

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 (K)-Specific Demethylase 5D) is a Protein Coding gene. Diseases associated with KDM5D include y chromosome infertility. 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.

Gene Wiki entry for KDM5D Gene

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

Genomics for KDM5D Gene

Genomic Location for KDM5D Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM5D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM5D Gene

Regulatory Elements 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; Note=Binds 1 Fe(2+) ion per subunit.;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Interacts with PCGF6 and MSH5.
    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

Proteomics data for KDM5D Gene at MOPED

Post-translational modifications for KDM5D Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys91, Lys101, Lys413, Lys729, Lys752, Lys766, Lys1101, and Lys1281

Domains for KDM5D Gene

Gene Families for KDM5D Gene

HGNC:
  • PHF :Zinc fingers, PHD-type
  • KDM :Chromatin-modifying enzymes / K-demethylases

UniProtKB/Swiss-Prot:

KDM5D_HUMAN
Domain:
  • The JmjC domain is required for enzymatic activity:
    • Q9BY66
  • Contains 1 ARID domain.:
    • Q9BY66
  • Contains 1 JmjC domain.:
    • Q9BY66
  • Contains 1 JmjN domain.:
    • Q9BY66
Family:
  • Belongs to the JARID1 histone demethylase family.:
    • Q9BY66
Similarity:
  • Contains 2 PHD-type zinc fingers.:
    • Q9BY66
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.

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:0005515 protein binding --
GO:0008270 zinc ion binding 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:0032453 histone demethylase activity (H3-K4 specific) IDA 17320160
genes like me logo Genes that share ontologies with KDM5D: view
genes like me logo Genes that share phenotypes with KDM5D: view

miRNA for KDM5D Gene

miRTarBase miRNAs that target KDM5D

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

Localization for KDM5D Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM5D Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM5D Gene COMPARTMENTS Subcellular localization image for KDM5D gene
Compartment Confidence
nucleus 4
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:0005622 intracellular --
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM5D: view

Pathways for KDM5D Gene

SuperPathways for KDM5D Gene

No Data Available

Gene Ontology (GO) - Biological Process for KDM5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0034720 histone H3-K4 demethylation IDA 17320160
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM5D: view

No data available for Pathways by source for KDM5D Gene

Compounds for KDM5D Gene

(1) Drugbank Compounds for KDM5D Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Vitamin C
  • Ascorbate
50-81-7 target
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:

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 for KDM5D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM5D Gene

SOURCE GeneReport for Unigene cluster for KDM5D Gene Hs.80358

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

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 36
  • 99.35 (n)
  • 99.02 (a)
KDM5D 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm5d 36
  • 80.33 (n)
  • 80.94 (a)
Kdm5d 16
Kdm5d 37
  • 80 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 37
  • 73 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 81 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 74 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii kdm5c 37
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta lid 37
  • 34 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rbr-2 37
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 37
  • 29 (a)
OneToMany
JHD2 39
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9938 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 41 (a)
OneToMany
Species with no ortholog for KDM5D:
  • 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 MAF
rs1050806 -- 19,710,403(-) CCCTG(C/T)GCCAT synonymous-codon, reference, utr-variant-3-prime, nc-transcript-variant
rs1050807 - 19,707,590(-) TGGGA(C/G)TTCTG missense, reference, nc-transcript-variant
rs1050808 -- 19,707,292(-) GGCCT(C/T)TGAAG reference, missense, nc-transcript-variant
rs1131326 -- 19,710,451(-) CTGAC(C/G/T)TTGAC reference, synonymous-codon, utr-variant-3-prime, nc-transcript-variant
rs2032580 -- 19,720,080(+) AAAAA(-/A)TATAA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv10025 CNV Gain 18304495

Relevant External Links for KDM5D Gene

HapMap Linkage Disequilibrium report
KDM5D

Disorders for KDM5D Gene

(1) MalaCards Diseases for KDM5D Gene

Search for KDM5D Gene in MalaCards »
genes like me logo Genes that share disorders with KDM5D: view

No data available for UniProtKB/Swiss-Prot 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
  2. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T. … Nomura N. (DNA Res. 1996) 3 4
  3. Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven. (PMID: 9060413) Agulnik A.I. … Solovyev V.V. (Mamm. Genome 1997) 3 4
  4. Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission. (PMID: 15613541) Miklos D.B. … Ritz J. (Blood 2005) 3 23
  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

Products for KDM5D Gene

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Polycomb & Trithorax Complexes in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate KDM5D
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for KDM5D
    • Block miRNA regulation of KDM5D using miScript Target Protectors

    Sources for KDM5D Gene

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