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KDM5D lysine demethylase 5D [ Homo sapiens (human) ]

Gene ID: 8284, updated on 26-May-2016
Official Symbol
KDM5Dprovided by HGNC
Official Full Name
lysine demethylase 5Dprovided by HGNC
Primary source
HGNC:HGNC:11115
See related
Ensembl:ENSG00000012817 HPRD:02464; MIM:426000; Vega:OTTHUMG00000036508
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HY; HYA; SMCY; JARID1D
Summary
This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Orthologs
Location:
Yq11
Exon count:
29
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) Y NC_000024.10 (19705415..19744939, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (21867301..21906825, complement)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377223 Neighboring gene taxilin gamma pseudogene, Y-linked Neighboring gene uncharacterized LOC105377224 Neighboring gene zinc finger protein 886, pseudogene Neighboring gene regulator of chromosome condensation 2 pseudogene 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Clone Names

  • KIAA0234

Gene Ontology Provided by GOA

Process Evidence Code Pubs
T cell antigen processing and presentation IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
lysine-specific demethylase 5D
Names
H-Y
Jumonji, AT rich interactive domain 1D (RBP2-like)
SMC homolog, Y chromosome
Smcy homolog, Y-linked
histocompatibility Y antigen
histone demethylase JARID1D
jumonji/ARID domain-containing protein 1D
lysine (K)-specific demethylase 5D
protein SmcY
selected mouse cDNA on Y, human homolog of

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.

Genomic

  1. NG_032920.1 RefSeqGene

    Range
    5001..44525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146705.1NP_001140177.1  lysine-specific demethylase 5D isoform 1

    See identical proteins and their annotated locations for NP_001140177.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA864889, BC144102, BC146767, DA940867
    Consensus CDS
    CCDS55555.1
    UniProtKB/Swiss-Prot
    Q9BY66
    Related
    ENSP00000444293, ENST00000541639
    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:522638
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:728781
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7921118
    PLU-1; PLU-1-like protein
    cd15604
    Location:316361
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:12051265
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
  2. NM_001146706.1NP_001140178.1  lysine-specific demethylase 5D isoform 3

    See identical proteins and their annotated locations for NP_001140178.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons in the coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AA864889, BC132721, BC144102, BC146767, DA940867
    Consensus CDS
    CCDS55554.1
    UniProtKB/Swiss-Prot
    Q9BY66
    Related
    ENSP00000372256, OTTHUMP00000034665, ENST00000382806, OTTHUMT00000088791
    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:434550
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:640693
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7041030
    PLU-1; PLU-1-like protein
    cl02633
    Location:76117
    ARID; ARID/BRIGHT DNA binding domain
    cd15604
    Location:259304
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11171177
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
  3. NM_004653.4NP_004644.2  lysine-specific demethylase 5D isoform 2

    See identical proteins and their annotated locations for NP_004644.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AA864889, BC132721, BC146767, DA940867, U52191
    Consensus CDS
    CCDS14794.1
    UniProtKB/Swiss-Prot
    Q9BY66
    Related
    ENSP00000322408, OTTHUMP00000034664, ENST00000317961, OTTHUMT00000088790
    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:697750
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7611087
    PLU-1; PLU-1-like protein
    cd15604
    Location:316361
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11741234
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p2 Primary Assembly

    Range
    19705415..19744939 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262560.1XP_005262617.1  

    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:446562
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:652705
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7161042
    PLU-1; PLU-1-like protein
    cd15604
    Location:271316
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11291189
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
  2. XM_005262561.1XP_005262618.1  

    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:697750
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7611010
    PLU-1; PLU-1-like protein
    cd15604
    Location:316361
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:10971157
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
  3. XM_011531468.1XP_011529770.1  

    Conserved Domains (7) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:697750
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7611083
    PLU-1; PLU-1-like protein
    cd15604
    Location:316361
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11481208
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
  4. XM_005262562.2XP_005262619.1  

    See identical proteins and their annotated locations for XP_005262619.1

    UniProtKB/TrEMBL
    B4E1Y0
    Conserved Domains (5) summary
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    pfam01388
    Location:76165
    ARID; ARID/BRIGHT DNA binding domain
    pfam02928
    Location:697750
    zf-C5HC2; C5HC2 zinc finger
    cd15604
    Location:316361
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)

RNA

  1. XR_430568.2 RNA Sequence

  2. XR_244571.2 RNA Sequence

  3. XR_938609.1 RNA Sequence

  4. XR_938610.1 RNA Sequence