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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:897788-943811 bp, + strand
From NCBI annotation of GRCm38

  46024 bp   ±  kb flank

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

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

Human
homologs
Human Homolog KDM5D, lysine (K)-specific demethylase 5D
NCBI Gene ID 8284
neXtProt AC  NX_Q9BY66
Human Synonyms  HY, HYA, JARID1D, SMCY
Human Chr (Location)  Yq11; chrY:19703865-19744939 (-)  GRCh38
Disease Associations  (1) Diseases Associated with Human KDM5D
Alleles
and
phenotypes
Incidental mutations (data from Mutagenetix , APF )
Gene Ontology
(GO)
classifications
All GO classifications: (21 annotations)
Process chromatin modification, histone H3-K4 demethylation, ...
Component intracellular, nucleus
Function 2,4-dichlorophenoxyacetate alpha-ketoglutarate dioxygenase activity, C-19 gibberellin 2-beta-dioxygenase activity, ...
External Resources: FuncBase
Expression
Literature Summary: (10 records)
Data Summary: Results (122)    Tissues (73)    Images (6)
Theiler Stages: 2, 3, 4, 5, 11, 13, 14, 15, 17, 21, 23, 24, 28
Assay TypeResults
RNA in situ 70
Northern blot 15
RT-PCR 37
cDNA source data(37)
External Resources: Allen Institute   GEO   ArrayExpress
Molecular
reagents
All nucleic(61) Genomic(13) cDNA(41) Primer pair(6) Other(1)
Microarray probesets(5)
Other database
links
Ensembl Gene ModelENSMUSG00000056673 (Evidence)
Entrez Gene20592 (Evidence)
UniGene262676
DFCITC1583128, TC1589288
DoTSDT.101152825, DT.101364913, DT.110950253, DT.110950270, DT.483887, DT.91324177, DT.91367749
NIA Mouse Gene IndexU142654
EC1.14.11.-
Consensus CDS ProjectCCDS30541.1
International Mouse Knockout Project StatusKdm5d
Sequences
Representative SequencesLengthStrain/SpeciesFlank
genomic 20592 NCBI Gene Model | MGI Sequence Detail 46024 C57BL/6J ±  kb
transcript NM_011419 RefSeq | MGI Sequence Detail 5471 C57BL/6 
polypeptide Q62240 UniProt | EBI | MGI Sequence Detail 1548 Not Applicable 

For the selected sequences
All sequences(36) RefSeq(5) UniProt(3)
Polymorphisms All PCR and RFLP(2) : PCR(1) RFLP(1) SNPs within 2kb(44 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
Graphical View of Protein Domain Structure
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:205146 Praktiknjo SD, et al., Novel effects of chromosome Y on cardiac regulation, chromatin remodeling, and neonatal programming in male mice. Endocrinology. 2013 Dec;154(12):4746-56
All references(46)
Other
accession IDs
MGD-MRK-16566

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
07/01/2014
MGI 5.18
The Jackson Laboratory