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 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

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:21867301-21906825 (-)  GRCh37.p10
Disease Associations		(1) Diseases Associated with Human KDM5D

Gene Ontology (GO) classifications

All GO classifications: (14 annotations)

Process	chromatin modification, histone H3-K4 demethylation, ...
Component	intracellular, nucleus
Function	DNA binding, histone demethylase activity (H3-K4 specific), ...

External Resources: FuncBase

Expression

Literature Summary: (9 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 Type	Results
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 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 Knockout Project Status	Kdm5d

Sequences

Length	Strain/Species
genomic	20592	NCBI Gene Model | MGI Sequence Detail	46024	C57BL/6J
transcript	NM_011419	RefSeq | MGI Sequence Detail	5471	C57BL/6
polypeptide	Q62240	UniProt | EBI | MGI Sequence Detail	1548	Not Applicable

All sequences(33) RefSeq(2) UniProt(3)

Polymorphisms

All PCR and RFLP(2) : PCR(1) RFLP(1) SNPs(9 from dbSNP Build 128)

Protein-related information

Resource	ID	Description
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	histone demethylase JARID1D

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:140465 Guo G, et al., Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell. 2010 Apr 20;18(4):675-85
All references(44)

Other accession IDs

MGD-MRK-16566