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Kdm5d lysine (K)-specific demethylase 5D [ Mus musculus (house mouse) ]

Gene ID: 20592, updated on 8-May-2016
Official Symbol
Kdm5dprovided by MGI
Official Full Name
lysine (K)-specific demethylase 5Dprovided by MGI
Primary source
MGI:MGI:99780
See related
Ensembl:ENSMUSG00000056673
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
HY; Smcy; Jarid1d
Location:
Y; Y A1
Exon count:
26
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) Y NC_000087.7 (897660..943813)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) Y NC_000087.6 (234231..280254)

Chromosome Y - NC_000087.7Genomic Context describing neighboring genes Neighboring gene ubiquitin-activating enzyme, Chr Y Neighboring gene ras homolog A translocated to the Y, pseudogene 3 Neighboring gene predicted gene, 39554 Neighboring gene predicted gene, 39553

Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
2,4-dichlorophenoxyacetate alpha-ketoglutarate dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
C-19 gibberellin 2-beta-dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
C-20 gibberellin 2-beta-dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-N1-methyladenine dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity (H3-K4 specific) ISO
Inferred from Sequence Orthology
more info
 
hypophosphite dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
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
Inferred from Electronic Annotation
more info
 
procollagen-proline dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
sulfonate dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
T cell antigen processing and presentation IDA
Inferred from Direct Assay
more info
PubMed 
chromatin modification IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 demethylation ISO
Inferred from Sequence Orthology
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
lysine-specific demethylase 5D
Names
H-Y
histocompatibility Y antigen
histone demethylase JARID1D
jumonji, AT rich interactive domain 1D (Rbp2 like)
jumonji/ARID domain-containing protein 1D
protein SmcY
selected mouse cDNA on the Y

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_011419.3NP_035549.1  lysine-specific demethylase 5D

    See identical proteins and their annotated locations for NP_035549.1

    Status: VALIDATED

    Source sequence(s)
    AB221607, AC134433, AC145392, BB647801, BQ921842, CA316252, CF728912
    Consensus CDS
    CCDS30541.1
    UniProtKB/Swiss-Prot
    Q62240
    Related
    ENSMUSP00000061095, OTTMUSP00000066308, ENSMUST00000055032, OTTMUST00000118913
    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500616
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:706759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7701096
    PLU-1; PLU-1-like protein
    cd15604
    Location:325370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cl22851
    Location:11821242
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000087.7 Reference GRCm38.p3 C57BL/6J

    Range
    897660..943813
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011248580.1XP_011246882.1  

    Conserved Domains (7) summary
    smart00545
    Location:1350
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:474590
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:51139
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:680733
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7441070
    PLU-1; PLU-1-like protein
    cd15604
    Location:299344
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cl22851
    Location:11561216
    PHD_SF; PHD finger superfamily
  2. XM_006531578.2XP_006531641.1  

    Conserved Domains (3) summary
    pfam02928
    Location:2780
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:91417
    PLU-1; PLU-1-like protein
    cl22851
    Location:503563
    PHD_SF; PHD finger superfamily

Alternate Mm_Celera

Genomic

  1. AC_000043.1 Alternate Mm_Celera

    Range
    3732939..3779374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)