Kdm8 (lysine demethylase 8) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Kdm8 (lysine demethylase 8) Heterocephalus glaber
Analyze
Symbol: Kdm8
Name: lysine demethylase 8
RGD ID: 18929142
Description: ENCODES a protein that exhibits aminopeptidase activity (ortholog); chromatin binding (ortholog); endopeptidase activity (ortholog); INVOLVED IN circadian regulation of gene expression (ortholog); fibroblast proliferation (ortholog); G2/M transition of mitotic cell cycle (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH breast cancer (ortholog); Coffin-Siris syndrome (ortholog); hepatocellular carcinoma (ortholog); FOUND IN cytosol (ortholog); nucleoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: JmjC domain-containing protein 5; lysine-specific demethylase 8
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478211,884,631 - 11,903,947 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478211,884,847 - 11,903,944 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (ISO)
nucleoplasm  (ISO)
nucleus  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:21993625   PMID:30032202  


Genomics

Comparative Map Data
Kdm8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478211,884,631 - 11,903,947 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478211,884,847 - 11,903,944 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
KDM8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381627,203,526 - 27,221,768 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1627,203,508 - 27,221,768 (+)EnsemblGRCh38hg38GRCh38
GRCh371627,214,847 - 27,233,089 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361627,122,317 - 27,140,544 (+)NCBINCBI36Build 36hg18NCBI36
Celera1625,993,442 - 26,011,724 (+)NCBICelera
Cytogenetic Map16p12.1NCBI
HuRef1625,303,702 - 25,321,984 (+)NCBIHuRef
CHM1_11628,226,511 - 28,244,793 (+)NCBICHM1_1
T2T-CHM13v2.01627,482,139 - 27,500,381 (+)NCBIT2T-CHM13v2.0
Kdm8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397125,043,788 - 125,062,823 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7125,043,848 - 125,061,441 (+)EnsemblGRCm39 Ensembl
GRCm387125,444,620 - 125,463,651 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7125,444,676 - 125,462,269 (+)EnsemblGRCm38mm10GRCm38
MGSCv377132,588,190 - 132,605,773 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367125,235,824 - 125,253,407 (+)NCBIMGSCv36mm8
Celera7125,303,361 - 125,320,954 (+)NCBICelera
Cytogenetic Map7F3NCBI
cM Map768.85NCBI
Kdm8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81189,444,527 - 189,459,507 (+)NCBIGRCr8
mRatBN7.21180,013,969 - 180,028,829 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1180,020,656 - 180,028,841 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1188,350,526 - 188,365,400 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01195,536,557 - 195,551,431 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01188,219,849 - 188,234,719 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01196,838,460 - 196,854,192 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1196,839,321 - 196,854,180 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01203,825,823 - 203,840,790 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,510,173 - 184,525,036 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,666,742 - 184,674,917 (+)NCBI
Celera1177,684,363 - 177,699,127 (+)NCBICelera
Cytogenetic Map1q36NCBI
Kdm8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554935,437,090 - 5,462,294 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554935,437,344 - 5,462,849 (+)NCBIChiLan1.0ChiLan1.0
KDM8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21828,602,178 - 28,620,254 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11633,142,252 - 33,160,327 (+)NCBINHGRI_mPanPan1
PanPan1.11627,577,230 - 27,595,164 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1627,577,230 - 27,595,164 (+)Ensemblpanpan1.1panPan2
KDM8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1619,366,813 - 19,390,082 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl619,366,331 - 19,380,257 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha620,948,051 - 20,971,318 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0619,509,426 - 19,532,710 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl619,509,438 - 19,532,685 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1619,307,285 - 19,330,551 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0619,220,623 - 19,244,109 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0619,567,219 - 19,590,503 (-)NCBIUU_Cfam_GSD_1.0
Kdm8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344122,834,703 - 122,855,523 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650110,933,671 - 10,951,707 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650110,932,541 - 10,955,772 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl319,653,402 - 19,676,148 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1319,653,396 - 19,676,207 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2319,871,955 - 19,945,912 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KDM8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1524,907,345 - 24,927,028 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl524,907,657 - 24,928,995 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660684,770,483 - 4,789,136 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000022311   ⟹   ENSHGLP00000022100
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462478211,884,631 - 11,903,947 (+)Ensembl
RefSeq Acc Id: ENSHGLT00000022312   ⟹   ENSHGLP00000022101
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462478211,893,193 - 11,902,967 (+)Ensembl
RefSeq Acc Id: XM_004855987   ⟹   XP_004856044
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,866 - 11,903,944 (+)NCBI
RefSeq Acc Id: XM_004855988   ⟹   XP_004856045
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,864 - 11,903,944 (+)NCBI
RefSeq Acc Id: XM_004855989   ⟹   XP_004856046
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,863 - 11,903,944 (+)NCBI
RefSeq Acc Id: XR_002386582
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,850 - 11,902,893 (+)NCBI
RefSeq Acc Id: XR_002386583
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,847 - 11,902,908 (+)NCBI
RefSeq Acc Id: XR_002386584
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462478211,884,855 - 11,902,908 (+)NCBI
Protein Sequences
Protein RefSeqs XP_004856044 (Get FASTA)   NCBI Sequence Viewer  
  XP_004856045 (Get FASTA)   NCBI Sequence Viewer  
  XP_004856046 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHB06321 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000022101
Reference Protein Sequences
RefSeq Acc Id: XP_004856046   ⟸   XM_004855989
- Peptide Label: isoform X2
- UniProtKB: G5BAL0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004856045   ⟸   XM_004855988
- Peptide Label: isoform X1
- UniProtKB: G5BAL0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004856044   ⟸   XM_004855987
- Peptide Label: isoform X1
- UniProtKB: G5BAL0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000022101   ⟸   ENSHGLT00000022312
RefSeq Acc Id: ENSHGLP00000022100   ⟸   ENSHGLT00000022311


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000015770 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000022312 ENTREZGENE
Gene3D-CATH Cupin UniProtKB/TrEMBL
InterPro Cupin_8 UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
NCBI Gene Kdm8 ENTREZGENE
PANTHER BIFUNCTIONAL PEPTIDASE AND (3S)-LYSYL HYDROXYLASE JMJD7-RELATED UniProtKB/TrEMBL
  HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR-RELATED UniProtKB/TrEMBL
Pfam Cupin_8 UniProtKB/TrEMBL
PROSITE JMJC UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
UniProt G5BAL0 ENTREZGENE, UniProtKB/TrEMBL