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Kdm5d
Gene Detail
Symbol

Name
ID
Kdm5d
lysine (K)-specific demethylase 5D
MGI:99780
Synonyms
HY, Jarid1d, Smcy
Feature Type
protein coding gene
Genetic Map
Chromosome Y
cytoband p

Mapping data(8)
Sequence Map
ChrY:897788-956786 bp, + strand
From VEGA annotation of GRCm38

  58999 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer


Mouse Genome Browser
Vertebrate
homology
HomoloGene:55838  Vertebrate Homology Class
1 human; 1 mouse; 1 chimpanzee

HCOP human homology predictions: KDM5D
Protein SuperFamily: histone H3 lysine 4 demethylase (Jumonji/ARID domain-containing protein)
Gene Tree: Kdm5d

Human
homologs
KDM5D, lysine (K)-specific demethylase 5D
Orthology source: HGNC, HomoloGene

IDs:
NCBI Gene ID: 8284
neXtProt AC: NX_Q9BY66

Human Synonyms: HY, HYA, JARID1D, SMCY

Human Chr (Location): Yq11; chrY:19705415-19744939 (-)  GRCh38.p2

Disease Associations: (1) Diseases Associated with Human KDM5D

Mutations,
alleles, and
phenotypes
All mutations/alleles(1) : Spontaneous(1)
Genomic Mutations involving Kdm5d (1)
Incidental mutations (data from Mutagenetix , APF )
Interactions
Kdm5d interacts with 154 markers (Mir1a-1, Mir1a-2, Mir1b, ...)
Gene Ontology
(GO)
classifications
Expression
Literature Summary: (11 records)
Data Summary: Results (115)    Tissues (70)    Images (6)    Tissue x Stage Matrix (view)
Assay TypeResults
RNA in situ 70
Northern blot 15
RT-PCR 30
cDNA source data(37)
Other mouse links: Allen Institute   GEO   Expression Atlas
Molecular
reagents
All nucleic(61) Genomic(13) cDNA(41) Primer pair(6) Other(1)
Microarray probesets(5)
Other database
links
VEGA Gene Model OTTMUSG00000045277 (Evidence)
Ensembl Gene Model ENSMUSG00000056673 (Evidence)
Entrez Gene 20592 (Evidence)
UniGene 262676
DFCI TC1583128, TC1589288
DoTS DT.101152825, DT.101364913, DT.110950253, DT.110950270, DT.483887, DT.91324177, DT.91367749
NIA Mouse Gene Index U142654
EC 1.14.11.-
Consensus CDS Project CCDS30541.1
International Mouse Phenotyping Consortium Status Kdm5d
Sequences
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000045277 VEGA Gene Model | MGI Sequence Detail 58999 C57BL/6J ±  kb
transcript OTTMUST00000118913 VEGA | MGI Sequence Detail 7974 Not Applicable 
polypeptide OTTMUSP00000066308 VEGA | MGI Sequence Detail 1548 Not Applicable 

For the selected sequences
All sequences(63) RefSeq(6) UniProt(4)
Polymorphisms
All PCR and RFLP(2) : PCR(1) RFLP(1) SNPs within 2kb(48 from dbSNP Build 137)
Protein-related
information
ResourceIDDescription
InterPro IPR001606 ARID/BRIGHT DNA-binding domain
InterPro IPR003347 JmjC domain
InterPro IPR013637 Lysine-specific demethylase-like domain
InterPro IPR003349 Transcription factor jumonji, JmjN
InterPro IPR004198 Zinc finger, C5HC2-type
InterPro IPR011011 Zinc finger, FYVE/PHD-type
InterPro IPR019787 Zinc finger, PHD-finger
InterPro IPR001965 Zinc finger, PHD-type
InterPro IPR019786 Zinc finger, PHD-type, conserved site
InterPro IPR013083 Zinc finger, RING/FYVE/PHD-type
Protein Ontology PR:000009207 lysine-specific demethylase 5D
References
(Earliest) J:18900 Agulnik AI, et al., A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens. Hum Mol Genet. 1994 Jun;3(6):873-8
(Latest) J:215367 Shao GB, et al., Dynamic patterns of histone H3 lysine 4 methyltransferases and demethylases during mouse preimplantation development. In Vitro Cell Dev Biol Anim. 2014 Aug;50(7):603-13
All references(47)
Other
accession IDs
MGD-MRK-16566

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
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last database update
07/21/2015
MGI 5.22
The Jackson Laboratory