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Kdm5d Gene Detail
 Symbol
Name
ID
Kdm5d
lysine (K)-specific demethylase 5D
MGI:99780


Nomenclature History
Synonyms HY, Jarid1d, Smcy
Genetic Map
Chromosome Y
cytoband p
 
Mapping data( 8)
Sequence Map
ChrY:234231-280254 bp, + strand
(From NCBI annotation of NCBI Build 37)
Ensembl ContigView | UCSC Browser | NCBI Map Viewer

Mouse Genome Browser
Mammalian
homology
human; chimpanzee; horse    (Mammalian Orthology)
Protein SuperFamily: histone H3 lysine 4 demethylase (Jumonji/ARID domain-containing protein)
TreeFam: TF106476
Sequences
Representative Sequences Length Strain/Species Flank
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(31)
Polymorphisms All PCR and RFLP(2) : PCR(1) RFLP(1) SNPs within 2kb(20 from dbSNP Build 128)  
Gene Ontology
(GO)
classifications
All GO classifications: (13 annotations)
Process chromatin modification, oxidation reduction...
Component intracellular, nucleus...
Function DNA binding, iron ion binding...
External Resources: FuncBase
Expression Literature Summary: (8 records)
Data Summary: Assays (12)    Results (86)    Tissues (58)    Images (3)
Theiler Stages: 2,3,4,5,11,13,14,15,17,21,24,28
  Assay Type Assays   Results
      RT-PCR 7   37
      RNA in situ 3   34
      Northern blot 2   15
cDNA source data(37)
External Resources: Allen Brain Atlas  GEO  ArrayExpress 
Molecular
reagents
All nucleic(63) Genomic(13) cDNA(41) Primer pair(6) Other(3)
Microarray probesets(4)
Other database
links
Ensembl Gene Model ENSMUSG00000056673
DoTS DT.101152825, DT.101364913, DT.110950253, DT.110950270, DT.483887, DT.91324177, DT.91367749
Consensus CDS Project CCDS30541.1
UniGene 262676
DFCI TC1583128, TC1589288
NIA Mouse Gene Index U142654
Entrez Gene 20592
International Mouse Knockout Project Status Kdm5d
Protein
domains
InterPro ID Description
IPR001606 ARID/BRIGHT DNA-binding domain
IPR001965 Zinc finger, PHD-type
IPR003347 Transcription factor jumonji/aspartyl beta-hydroxylase
IPR003349 Transcription factor jumonji, JmjN
IPR004198 Zinc finger, C5HC2-type
IPR011011 Zinc finger, FYVE/PHD-type
IPR013129 Transcription factor jumonji
IPR013637 PLU-1-like
IPR019786 Zinc finger, PHD-type, conserved site
IPR019787 Zinc finger, PHD-finger
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:141291 Tamplin OJ et al., "Microarray analysis of Foxa2 mutant mouse embryoa reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives" BMC Genomics 2008;9(1):511
All references(24)
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
02/06/2010
MGI_4.32
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