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

Gene ID: 8284, updated on 3-Jan-2019

Summary

Official Symbol
KDM5Dprovided by HGNC
Official Full Name
lysine demethylase 5Dprovided by HGNC
Primary source
HGNC:HGNC:11115
See related
Ensembl:ENSG00000012817 MIM:426000
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]
Expression
Broad expression in small intestine (RPKM 5.6), prostate (RPKM 3.5) and 20 other tissues See more
Orthologs

Genomic context

See KDM5D in Genome Data Viewer
Location:
Yq11.223
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) Y NC_000024.10 (19705415..19745341, 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

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0234

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
androgen receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-trimethyl-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 demethylation, trimethyl-H3-K4-specific IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
regulation of androgen receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of androgen receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
fibrillar center IDA
Inferred from Direct Assay
more info
 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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
epididymis secretory sperm binding protein
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

NCBI Reference Sequences (RefSeq)

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
    ENSP00000444293.1, ENST00000541639.5
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:522638
    JmjC; JmjC domain, hydroxylase
    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)
    pfam02928
    Location:728780
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7931116
    PLU-1; PLU-1-like protein
  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
    ENSP00000372256.2, ENST00000382806.6
    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
    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)
    pfam02928
    Location:640692
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7051028
    PLU-1; PLU-1-like protein
    cl02633
    Location:80117
    ARID; ARID/BRIGHT DNA binding domain
  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
    ENSP00000322408.4, ENST00000317961.8
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    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)
    pfam02928
    Location:697749
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7621085
    PLU-1; PLU-1-like protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p12 Primary Assembly

    Range
    19705415..19745341 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452495.1XP_024308263.1  lysine-specific demethylase 5D isoform X4

    Conserved Domains (3) summary
    cd15608
    Location:504564
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:2779
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:92415
    PLU-1; PLU-1-like protein
  2. XM_005262560.3XP_005262617.1  lysine-specific demethylase 5D isoform X2

    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:446562
    JmjC; JmjC domain, hydroxylase
    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)
    pfam02928
    Location:652704
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7171040
    PLU-1; PLU-1-like protein
  3. XM_005262561.3XP_005262618.1  lysine-specific demethylase 5D isoform X3

    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    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)
    pfam02928
    Location:697749
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7621008
    PLU-1; PLU-1-like protein
  4. XM_011531468.3XP_011529770.1  lysine-specific demethylase 5D isoform X1

    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:491607
    JmjC; JmjC domain, hydroxylase
    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)
    pfam02928
    Location:697749
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7621083
    PLU-1; PLU-1-like protein
  5. XM_024452496.1XP_024308264.1  lysine-specific demethylase 5D isoform X5

    Conserved Domains (2) summary
    cd15608
    Location:426486
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam08429
    Location:14337
    PLU-1; PLU-1-like protein

RNA

  1. XR_001756011.2 RNA Sequence

  2. XR_244571.4 RNA Sequence

  3. XR_001756010.2 RNA Sequence

  4. XR_001756009.2 RNA Sequence

  5. XR_430568.4 RNA Sequence

  6. XR_001756013.2 RNA Sequence

  7. XR_001756012.2 RNA Sequence

  8. XR_002958834.1 RNA Sequence

  9. XR_002958837.1 RNA Sequence

  10. XR_002958836.1 RNA Sequence

  11. XR_002958835.1 RNA Sequence

  12. XR_002958832.1 RNA Sequence

  13. XR_002958833.1 RNA Sequence

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