KDM5D Gene
protein-coding GIFtS: 53
GC0YM020326
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lysine (K)-specific demethylase 5D (Previous names: Jumonji, AT rich interactive domain 1D (RBP2-like), Smcy homolog, Y-linked (mouse), jumonji, AT rich interactive domain 1D ) Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database (Previous symbols: HYA, HY, SMCY, JARID1D)
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Aliases & Descriptions for KDM5D
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
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| Aliases |
|---|
| EC 1.14.11.- 3 | | H-Y 3 | | HY 2, 3 | | HYA 2, 3 | | JARID1D 2, 3 | | KIAA0234 1, 2, 3 | | SMCY 2, 3 |
| | | Descriptions |
|---|
| Histocompatibility Y antigen 2, 3 | | Histone demethylase JARID1D 3 | | Jumonji, AT rich interactive domain 1D (RBP2-like) 1, 2 | | Jumonji/ARID domain-containing protein 1D 3 | | Protein SmcY 3 | | SMC homolog, Y chromosome 2 | | Smcy homolog, Y chromosome 2 | | Smcy homolog, Y-linked 2 | | Smcy homolog, Y-linked (mouse) 1 | | jumonji, AT rich interactive domain 1D 1, 2 | | lysine (K)-specific demethylase 5D 2 | | lysine-specific demethylase 5D 1 | | selected mouse cDNA on Y, human homolog of 2 |
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| | Search outside databases for aliases for KDM5D gene |
Summaries for KDM5D(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| EntrezGene summary for KDM5D: 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] UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesisGene Wiki entry for KDM5D (JARID1D) |
Genomic Location for KDM5D
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to
UCSC and
Ensembl,
Transcription factor binding sites according to
SABiosciences) About This Section
| Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: Yq11|Yq11 Ensembl cytogenetic band: Yq11.222 HGNC cytogenetic band: Yq11KDM5D Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)
 GeneLoc gene densities for chromosome Y GeneLoc Exon Structure GeneLoc location for GC0YM020326:
(about GC identifiers)
Start:
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20,326,689 bp from pter |
End:
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20,366,212 bp from pter |
Size:
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39,524 bases |
Orientation:
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minus strand |
RefSeq DNA sequence:- NC_000024.8 NT_011875.11
| Proteins for KDM5D
(According to
1UniProtKB,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Enzo Life Sciences,
Abnova,
OriGene and/or,
Abcam,
Biochemical Assays by
Invitrogen,
Millipore,
R&D Systems,
Cell Signaling Technology, and/or
Enzo Life Sciences,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene,
Antibodies by Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Cell Signaling Technology,
Abcam,
Abnova, and/or
Novus Biologicals)
About This Section
| UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66 (See
protein sequence)Recommended Name: Lysine-specific demethylase 5D Size: 1539 amino acids; 174073 Da
Cofactor: Ascorbate
Cofactor: Fe(2+)
Subunit: Interacts with PCGF6
Subcellular location: Nucleus (Probable)
PDB structure from and Proteopedia :2E6R (3D)
 2YQE (3D)
 
Secondary accessions: A2RU19 Q92509 Q92809 Q9HCU1Alternative splicing: 2 isoforms: Q9BY66-1 Q9BY66-2 (Additional isoforms seem to exist)Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (3 alternative transcripts):
NP_001140177.1 NP_001140178.1 NP_004644.2
ENSEMBL proteins: ENSP00000322408 ENSP00000372256
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
3 Gene Ontology (GO) cellular component terms (links to tree view): About this table
Antibodies for KDM5D: Assays for KDM5D: | Protein
Domains/ Families for KDM5D(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry Q9BY66
ProtoNet protein and cluster: Q9BY66 5/6 Blocks protein families (see all 6
): IPB001606 ARID (AT-rich interaction domain) protein IPB001965 Zn-finger-like IPB003347 Transcription factor jumonji IPB003349 Transcription factor jumonji IPB004198 Zn-finger
UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66Domain: The JmjC domain is required for enzymatic activitySimilarity: Belongs to the JARID1 histone demethylase familySimilarity: Contains 1 ARID domainSimilarity: Contains 1 JmjC domainSimilarity: Contains 1 JmjN domainSimilarity: Contains 2 PHD-type zinc fingers | Gene Function for KDM5D
(According to MGI Jun 06 2009, UniProtKB,
IUBMB,and/or Genatlas,
shRNA from
OriGene,
Sigma-Aldrich, RNAi from
Sigma-Aldrich,
RNAi Products,
Clones, and
Q-PCR Products
from Invitrogen,
Millipore,
OriGene, and/or
Abnova,
siRNAs from
Applied Biosystems,
SYBR primers from OriGene,
Cell-based Assays from Millipore,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004653
Applied Biosystems Silencer® siRNAs for KDM5D
Sigma-Aldrich siRNA and siRNA Panels for KDM5D  Sigma-Aldrich shRNA for KDM5D  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_004653                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_004653                                  untagged cDNA clone in CMV expression vector: NM_004653 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_004653
UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesisEnzyme Number (IUBMB): EC 1.14.11.- 5/8 Gene Ontology (GO) molecular function terms (links to tree view) (see all 8
): About this table | Pathways & Interactions for KDM5D
(Pathways according to Invitrogen
(maps by GeneGo),
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Proteins Network according to
SABiosciences,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
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Gene Network CentralTM Interacting Genes and Proteins Network for KDM5D 
5/23 Interacting proteins for KDM5D (ENSP000003224083 Q9BY661) via UniProtKB, MINT, and/or STRING (see all 23
)About this table
3 Gene Ontology (GO) biological process terms (links to tree view): About this table
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Drugs & Compounds for KDM5D(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
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Browse Tocris compounds for KDM5D
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Transcripts for KDM5D(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank, RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from Invitrogen,
Millipore, and/or
Abnova,
siRNAs from Applied Biosystems,
Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
Tagged/untagged cDNA clones from
OriGene, Expression Assays from Applied Biosystems) About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004653
Sigma-Aldrich siRNA and siRNA Panels for KDM5D  Sigma-Aldrich shRNA for KDM5D  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_004653 REFSEQ mRNAs for KDM5D gene (3 alternative transcripts): NM_001146705.1 NM_001146706.1 NM_004653.4
Applied Biosystems TaqMan ® Gene Expression Assays: NM_004653               OriGene GFP tagged cDNA clone in CMV expression vector: NM_004653                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_004653                                  untagged cDNA clone in CMV expression vector: NM_004653  Additional cDNA sequence: AK095923.1 AK304027.1 BC011053.1 BC132721.1 BC144101.1 BC144102.1 BC146767.1 BX648643.1 D87072.1 U52191.1 U52365.1 12 DOTS entries: DT.95159961 DT.40233810 DT.92046785 DT.100691331 DT.40131582 DT.120654025 DT.101957266 DT.120654022 DT.120654028 DT.120654029 DT.91978680 DT.95322478 24/87 AceView cDNA sequences (see all 87
):CD652272 AA262767 D87072 BI025365 AA215375 BM052719 BQ651915 BP367589 AA465521 U52365 CF552345 AI341366 AA377435 BX648643 BQ053814 AL043711 AA113921 NM_004653 AI660371 AV763928 AA846126 AA864889 CK903936 BU664887 Unigene Cluster for KDM5D: Lysine (K)-specific demethylase 5D Hs.80358 [show with all ESTs]Unigene Representative Sequence: BX648643
GeneLoc Exon Structure
5/10 Alternative Splicing Database (ASD) splice patterns (SP) for KDM5D (see all 10
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| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12a | · | 12b | · | 12c | ^ | 13 | ^ | 14a | · | 14b | ^ | 15 | ^ | 16 | ^ | 17a | · | 17b | ^ | 18a | · | 18b | · | 18c | ^ | 19a | · | |
| SP1: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | - |   | |   | |
| SP2: | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | - |   | |   | |
| SP3: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |
| SP4: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | - |   | |
| SP5: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   |
| ExUns: | 19b | ^ | 20a | · | 20b | ^ | 21 | ^ | 22 | ^ | 23a | · | 23b | ^ | 24a | · | 24b | ^ | 25 | ^ | 26a | · | 26b | · | 26c | ^ | 27 | ^ | 28a | · | 28b | ^ | 29a | · | 29b | |
| SP1: | |   | - |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP2: | |   | - |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP3: | |   | - |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP4: | - |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP5: | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   |
About this scheme
ECgene alternative splicing isoforms for KDM5D
2 Ensembl transcripts including schematic representations: ENST00000317961
ENST00000382806
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Expression for KDM5D
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Expression Assays from
Applied Biosystems
)
About This Section
| KDM5D expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for KDM5D
1 / 2 4 probe-sets matching KDM5D gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: ACTCTACCTG
SOURCE GeneReport for Unigene cluster: Hs.80358
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Orthologs for KDM5D
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
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Orthologs for KDM5D gene from 4 species
About this table Species with no ortholog for KDM5D
ENSEMBL Gene Tree for KDM5D | Paralogs for KDM5D(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| Paralogs for KDM5D gene
- KDM5C2 ENSG000001171392 KDM5A2
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SNPs/Variants for KDM5D(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
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Disorders & Mutations for KDM5D
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
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OMIM: 426000
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Medical News for KDM5D(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for KDM5D (in
PubMed.
Associations of this gene to articles via
1Novoseek,
2HGNC,
3Entrez Gene,
4UniProtKB/Swiss-Prot,
5UniProtKB/TrEMBL,
6GAD, and/or
7PharmGKB)
About This Section
| 10/36 PubMed articles for KDM5D gene (see all 36
):- Gene sequence and evolutionary conservation of human SMCY. (PubMed id 8841177)2, 3, 4 Kent-First M.G....VandeBerg J. (1996)
- Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. (PubMed id 17320162)3, 4 Lee M.G.... Shiekhattar R. (2007)
- The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. (PubMed id 17320160)3, 4 Iwase S.... Shi Y. (2007)
- Population genetic implications from sequence variation in four Y chromosome genes. (PubMed id 10861003)3, 4 Shen P.... Oefner P.J. (2000)
- Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven. (PubMed id 9060413)3, 4 Agulnik A.I.... Solovyev V.V. (1997)
- Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PubMed id 9039502)3, 4 Nagase T....Nomura N. (1996)
- Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein. (PubMed id 7667640)1, 3 Wang W....Bishop C.E. (1995)
- Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission. (PubMed id 15613541)1, 3 Miklos D.B....Ritz J. (2005)
- HA-1 and the SMCY-derived peptide FIDSYICQV (H-Y) are immunodominant minor histocompatibility antigens after bone marrow transplantation. (PubMed id 9798702)1, 3 Rufer N.... Roosnek E. (1998)
- The male-specific histocompatibility antigen, H-Y: a history of transplantation, immune response genes, sex determination and expression cloning. (PubMed id 9143681)1, 3 Simpson E....Chandler P. (1997)
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Search for KDM5D
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
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Genome Databases showing KDM5D
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing KDM5D
(According to HUGE)
About This Section
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Specialized Databases showing KDM5D(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
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| About This Section
| --
| Services for KDM5D(Reagents available from Applied Biosystems, Antibodies and assays by Cell
Signaling Technology, Abcam, Novus Biologicals, Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich, Enzo Life Sciences, and/or Tocris Bioscience) About This Section
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 Products for KDM5D:

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GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
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