Kdm5d (lysine demethylase 5D) - Rat Genome Database

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Gene: Kdm5d (lysine demethylase 5D) Rattus norvegicus
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Symbol: Kdm5d
Name: lysine demethylase 5D
RGD ID: 2314436
Description: Predicted to enable histone H3K4me/H3K4me2/H3K4me3 demethylase activity and nuclear androgen receptor binding activity. Predicted to be involved in chromatin remodeling; regulation of DNA-templated transcription; and regulation of androgen receptor signaling pathway. Predicted to act upstream of or within T cell antigen processing and presentation. Predicted to be located in fibrillar center. Predicted to be active in chromatin and nucleus. Orthologous to human KDM5D (lysine demethylase 5D); PARTICIPATES IN histone modification pathway; INTERACTS WITH alpha-Zearalanol; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Jarid1d; LOC103694547; lysine (K)-specific demethylase 5D; lysine-specific demethylase 5D; uncharacterized LOC103694547
RGD Orthologs
Human
Mouse
Bonobo
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8Y551,621 - 647,742 (+)NCBIGRCr8
mRatBN7.2Y527,069 - 624,019 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblY530,401 - 624,018 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0Y501,058 - 589,267 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY505,996 - 589,267 (+)EnsemblRnor6.0rn6Rnor6.0
Cytogenetic MapYq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16301625   PMID:17320160   PMID:20333173   PMID:24759410   PMID:27185910  


Genomics

Comparative Map Data
Kdm5d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8Y551,621 - 647,742 (+)NCBIGRCr8
mRatBN7.2Y527,069 - 624,019 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblY530,401 - 624,018 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0Y501,058 - 589,267 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY505,996 - 589,267 (+)EnsemblRnor6.0rn6Rnor6.0
Cytogenetic MapYq11NCBI
KDM5D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38Y19,703,865 - 19,744,726 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblY19,703,865 - 19,744,939 (-)EnsemblGRCh38hg38GRCh38
GRCh37Y21,865,751 - 21,906,612 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y20,326,689 - 20,366,212 (-)NCBINCBI36Build 36hg18NCBI36
Build 34Y20,255,427 - 20,294,949NCBI
CeleraY5,866,720 - 5,906,241 (+)NCBICelera
Cytogenetic MapYq11.223NCBI
HuRefY15,577,021 - 15,616,789 (-)NCBIHuRef
T2T-CHM13v2.0Y20,610,415 - 20,651,276 (-)NCBIT2T-CHM13v2.0
Kdm5d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39Y897,566 - 946,316 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblY897,788 - 956,786 (+)EnsemblGRCm39 Ensembl
GRCm38Y897,566 - 943,813 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblY897,788 - 956,786 (+)EnsemblGRCm38mm10GRCm38
MGSCv37Y234,231 - 280,254 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36Y234,231 - 280,254 (+)NCBIMGSCv36mm8
CeleraY3,732,939 - 3,779,374 (+)NCBICelera
Cytogenetic MapYpterNCBI
KDM5D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2Y36,282,210 - 36,322,055 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1Y10,604,951 - 10,644,006 (-)NCBINHGRI_mPanPan1
LOC110257883
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblY39,582,815 - 39,631,815 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1Y39,582,253 - 39,631,823 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Variants

.
Variants in Kdm5d
270 total Variants

Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 9 43 100 86 87 58 21 58 6 202 85 82 44 46 29

Sequence


Ensembl Acc Id: ENSRNOT00000086056   ⟹   ENSRNOP00000073953
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY530,401 - 624,018 (+)Ensembl
Rnor_6.0 EnsemblY506,149 - 589,242 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblY573,756 - 583,376 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093053
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY616,871 - 620,874 (+)Ensembl
Rnor_6.0 EnsemblY582,087 - 586,124 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093125   ⟹   ENSRNOP00000076027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblY505,996 - 589,267 (+)Ensembl
RefSeq Acc Id: NM_001419852   ⟹   NP_001406781
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y564,486 - 647,742 (+)NCBI
mRatBN7.2Y540,760 - 624,019 (+)NCBI
RefSeq Acc Id: XM_008773689   ⟹   XP_008771911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y556,819 - 647,742 (+)NCBI
mRatBN7.2Y527,900 - 624,019 (+)NCBI
Rnor_6.0Y505,875 - 589,267 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100687   ⟹   XP_038956615
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y631,315 - 647,742 (+)NCBI
mRatBN7.2Y607,591 - 624,019 (+)NCBI
RefSeq Acc Id: XM_063280592   ⟹   XP_063136662
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y551,621 - 647,742 (+)NCBI
RefSeq Acc Id: XM_063280593   ⟹   XP_063136663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8Y551,621 - 631,791 (+)NCBI
RefSeq Acc Id: XP_008771911   ⟸   XM_008773689
- Peptide Label: isoform X2
- UniProtKB: W8C8J2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000076027   ⟸   ENSRNOT00000093125
Ensembl Acc Id: ENSRNOP00000073953   ⟸   ENSRNOT00000086056
RefSeq Acc Id: XP_038956615   ⟸   XM_039100687
- Peptide Label: isoform X3
- UniProtKB: V9GVE9 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001406781   ⟸   NM_001419852
- UniProtKB: W8C8J2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136662   ⟸   XM_063280592
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K6V2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136663   ⟸   XM_063280593
- Peptide Label: isoform X4
Protein Domains
ARID   JmjC   JmjN   Lysine-specific demethylase-like   PHD-type   Zinc finger PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-W8C8J2-F1-model_v2 AlphaFold W8C8J2 1-1550 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13702079
Promoter ID:EPDNEW_R12600
Type:multiple initiation site
Name:Kdm5d_1
Description:lysine demethylase 5D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0Y505,989 - 506,049EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2314436 AgrOrtholog
BioCyc Gene G2FUF-589 BioCyc
Ensembl Genes ENSRNOG00000060496 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086056.3 UniProtKB/TrEMBL
  ENSRNOT00000093053.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
InterPro ARID_dom UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  Lys_sp_deMease_like_dom UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_C5HC2 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 100312983 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 5D UniProtKB/TrEMBL
Pfam ARID UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  zf-C5HC2 UniProtKB/TrEMBL
PhenoGen Kdm5d PhenoGen
PROSITE ARID UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000060496 RatGTEx
SMART ARID UniProtKB/TrEMBL
  BRIGHT UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  SSF46774 UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt A0A0G2K6V2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZLH9_RAT UniProtKB/TrEMBL
  C9WPN4_RAT UniProtKB/TrEMBL
  V9GVE9 ENTREZGENE, UniProtKB/TrEMBL
  W8C8J2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Kdm5d  lysine demethylase 5D  LOC103694547  uncharacterized LOC103694547  Data merged from RGD:9270267 737654 PROVISIONAL
2016-02-17 Kdm5d  lysine demethylase 5D  Kdm5d  lysine (K)-specific demethylase 5D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694547  uncharacterized LOC103694547      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-11-13 Kdm5d  lysine (K)-specific demethylase 5D      Symbol and Name status set to provisional 70820 PROVISIONAL