Human Gene KDM5D (ENST00000317961.9_14) from GENCODE V47lift37
  Description: lysine demethylase 5D, transcript variant 2 (from RefSeq NM_004653.5)
Gencode Transcript: ENST00000317961.9_14
Gencode Gene: ENSG00000012817.16_17
Transcript (Including UTRs)
   Position: hg19 chrY:21,865,751-21,906,612 Size: 40,862 Total Exon Count: 27 Strand: -
Coding Region
   Position: hg19 chrY:21,867,881-21,906,420 Size: 38,540 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrY:21,865,751-21,906,612)mRNA (may differ from genome)Protein (1539 aa)
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-  Comments and Description Text from UniProtKB
  ID: KDM5D_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 5D; EC=1.14.11.-; AltName: Full=Histocompatibility Y antigen; Short=H-Y; AltName: Full=Histone demethylase JARID1D; AltName: Full=Jumonji/ARID domain-containing protein 1D; AltName: Full=Protein SmcY;
FUNCTION: 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 spermatogenesis.
COFACTOR: Ascorbate.
COFACTOR: Binds 1 Fe(2+) ion per subunit.
SUBUNIT: Interacts with PCGF6 and MSH5.
SUBCELLULAR LOCATION: Nucleus (Probable).
DOMAIN: The JmjC domain is required for enzymatic activity.
SIMILARITY: Belongs to the JARID1 histone demethylase family.
SIMILARITY: Contains 1 ARID domain.
SIMILARITY: Contains 1 JmjC domain.
SIMILARITY: Contains 1 JmjN domain.
SIMILARITY: Contains 2 PHD-type zinc fingers.
SEQUENCE CAUTION: Sequence=BAA13241.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.15 RPKM in Spleen
Total median expression: 651.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.4075-0.205 Picture PostScript Text
3' UTR -492.702130-0.231 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001606 - ARID/BRIGHT_DNA-bd
IPR003347 - JmjC_dom
IPR013637 - Lys_sp_deMease_like_dom
IPR003349 - TF_JmjN
IPR019786 - Zinc_finger_PHD-type_CS
IPR004198 - Znf_C5HC2
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF01388 - ARID/BRIGHT DNA binding domain
PF02373 - JmjC domain, hydroxylase
PF02375 - jmjN domain
PF02928 - C5HC2 zinc finger
PF08429 - PLU-1-like protein

SCOP Domains:
46774 - ARID-like
51197 - Clavaminate synthase-like
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2E6R - NMR MuPIT 2YQE - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9BY66
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0032452 histone demethylase activity
GO:0032453 histone demethylase activity (H3-K4 specific)
GO:0046872 metal ion binding
GO:0050681 androgen receptor binding
GO:0051213 dioxygenase activity

Biological Process:
GO:0002457 T cell antigen processing and presentation
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0034720 histone H3-K4 demethylation
GO:0055114 oxidation-reduction process
GO:0060765 regulation of androgen receptor signaling pathway

Cellular Component:
GO:0001650 fibrillar center
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC146767 - Homo sapiens jumonji, AT rich interactive domain 1D, mRNA (cDNA clone MGC:166841 IMAGE:9007211), complete cds.
D87072 - Homo sapiens mRNA for KIAA0234 gene.
U52191 - Human SMCY (H-Y) mRNA, complete cds.
BC132721 - Homo sapiens jumonji, AT rich interactive domain 1D, mRNA (cDNA clone MGC:164352 IMAGE:40146743), complete cds.
BC144101 - Homo sapiens cDNA clone IMAGE:9052621.
BC144102 - Homo sapiens jumonji, AT rich interactive domain 1D, mRNA (cDNA clone MGC:177639 IMAGE:9052622), complete cds.
GQ900944 - Homo sapiens clone HEL-T-56 epididymis secretory sperm binding protein mRNA, complete cds.
AB384449 - Synthetic construct DNA, clone: pF1KA0234, Homo sapiens JARID1D gene for histone demethylase JARID1D, complete cds, without stop codon, in Flexi system.
AK304027 - Homo sapiens cDNA FLJ61048 complete cds, highly similar to Jumonji/ARID domain-containing protein 1D.
BC011053 - Homo sapiens jumonji, AT rich interactive domain 1D, mRNA (cDNA clone IMAGE:4339613), with apparent retained intron.
BX648643 - Homo sapiens mRNA; cDNA DKFZp686O17106 (from clone DKFZp686O17106).
AK127269 - Homo sapiens cDNA FLJ45336 fis, clone BRHIP3007609, highly similar to Jumonji/ARID domain-containing protein 1D.
JD433466 - Sequence 414490 from Patent EP1572962.
AK095923 - Homo sapiens cDNA FLJ38604 fis, clone HEART2004570, highly similar to SMC.
JD404193 - Sequence 385217 from Patent EP1572962.
JD522006 - Sequence 503030 from Patent EP1572962.
JD092884 - Sequence 73908 from Patent EP1572962.
JD054038 - Sequence 35062 from Patent EP1572962.
JD115446 - Sequence 96470 from Patent EP1572962.
JD553836 - Sequence 534860 from Patent EP1572962.
JD347503 - Sequence 328527 from Patent EP1572962.
JD541632 - Sequence 522656 from Patent EP1572962.
JD047872 - Sequence 28896 from Patent EP1572962.
U52365 - Human SMCY mRNA, partial cds.
JD206870 - Sequence 187894 from Patent EP1572962.
JD216673 - Sequence 197697 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BY66 (Reactome details) participates in the following event(s):

R-HSA-4754181 KDM5A-D demethylate Me2K5-histone H3
R-HSA-5661116 KDM5A-D demethylate Me3K5-histone H3
R-HSA-3214842 HDMs demethylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: A2RU19, A6H8V7, B7ZLX1, ENST00000317961.1, ENST00000317961.2, ENST00000317961.3, ENST00000317961.4, ENST00000317961.5, ENST00000317961.6, ENST00000317961.7, ENST00000317961.8, HY, HYA, JARID1D, KDM5D_HUMAN, KIAA0234, NM_004653, Q92509, Q92809, Q9BY66, Q9HCU1, SMCY, uc317qjb.1, uc317qjb.2
UCSC ID: ENST00000317961.9_14
RefSeq Accession: NM_004653.5
Protein: Q9BY66 (aka KDM5D_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.