Cd63 (Cd63 molecule) - Rat Genome Database

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Gene: Cd63 (Cd63 molecule) Rattus norvegicus
Analyze
Symbol: Cd63
Name: Cd63 molecule
RGD ID: 62080
Description: Involved in several processes, including negative regulation of epithelial cell migration; positive regulation of cell adhesion; and positive regulation of endocytosis. Localizes to several cellular components, including extracellular exosome; lysosome; and plasma membrane. Orthologous to human CD63 (CD63 molecule); INTERACTS WITH 1-naphthyl isothiocyanate; 3H-1,2-dithiole-3-thione; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CD63 antigen; mast cell antigen AD1; MGC72893
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.271,325,108 - 1,340,447 (+)NCBI
Rnor_6.0 Ensembl73,320,103 - 3,335,582 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.073,320,250 - 3,335,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.073,303,449 - 3,305,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.472,208,659 - 2,211,323 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.172,208,658 - 2,211,327 (+)NCBI
Celera71,208,422 - 1,211,249 (+)NCBICelera
Cytogenetic Map7q11NCBI
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
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methylcholine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
5-fluorouracil  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
carbon nanotube  (ISO)
ceric oxide  (ISO)
chloropicrin  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
ciprofibrate  (ISO)
cisplatin  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
dibenz[a,h]anthracene  (EXP)
dibutyl phthalate  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenbuconazole  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
glyphosate  (ISO)
hexachlorobenzene  (EXP)
hydralazine  (ISO)
isobutanol  (ISO)
L-methionine  (ISO)
metformin  (EXP)
methylmercury(1+)  (EXP)
N-formyl-L-methionyl-L-leucyl-L-phenylalanine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
pyrene  (EXP)
quercetin  (ISO)
rotenone  (EXP,ISO)
SB 203580  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
valproic acid  (ISO)
vitamin E  (ISO)
Yessotoxin  (ISO)
zinc oxide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Additional References at PubMed
PMID:1302249   PMID:1703158   PMID:12477932   PMID:12519789   PMID:14668490   PMID:15229288   PMID:15489334   PMID:15647390   PMID:15908444   PMID:16917503   PMID:17897319   PMID:19056867  
PMID:21149578   PMID:21505438   PMID:21962903   PMID:22431521   PMID:22660413   PMID:23092844   PMID:23376485   PMID:23533145   PMID:23632027   PMID:24038174   PMID:25645918   PMID:26280656  
PMID:27435297   PMID:30021215   PMID:30121936   PMID:30871575  


Genomics

Comparative Map Data
Cd63
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.271,325,108 - 1,340,447 (+)NCBI
Rnor_6.0 Ensembl73,320,103 - 3,335,582 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.073,320,250 - 3,335,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.073,303,449 - 3,305,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.472,208,659 - 2,211,323 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.172,208,658 - 2,211,327 (+)NCBI
Celera71,208,422 - 1,211,249 (+)NCBICelera
Cytogenetic Map7q11NCBI
CD63
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1255,725,323 - 55,729,707 (-)EnsemblGRCh38hg38GRCh38
GRCh381255,725,323 - 55,729,673 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371256,119,107 - 56,123,457 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,405,497 - 54,409,177 (-)NCBINCBI36hg18NCBI36
Build 341254,405,519 - 54,409,076NCBI
Celera1255,771,700 - 55,775,380 (-)NCBI
Cytogenetic Map12q13.2NCBI
HuRef1253,158,042 - 53,162,273 (-)NCBIHuRef
CHM1_11256,086,015 - 56,090,245 (-)NCBICHM1_1
Cd63
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,731,577 - 128,748,691 (+)NCBIGRCm39mm39
GRCm39 Ensembl10128,736,858 - 128,748,691 (+)Ensembl
GRCm3810128,896,231 - 128,912,822 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,900,989 - 128,912,822 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710128,345,975 - 128,349,878 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610128,312,873 - 128,315,771 (+)NCBImm8
Celera10131,301,602 - 131,305,504 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1077.19NCBI
Cd63
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,362,511 - 3,363,981 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,362,511 - 3,363,916 (-)NCBIChiLan1.0ChiLan1.0
CD63
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11233,906,343 - 33,910,595 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1233,906,314 - 33,910,595 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01233,181,896 - 33,186,123 (+)NCBIMhudiblu_PPA_v0panPan3
CD63
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110126,370 - 139,301 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10126,449 - 129,742 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10188,764 - 191,664 (-)NCBI
ROS_Cfam_1.010133,644 - 136,544 (-)NCBI
UMICH_Zoey_3.110111,323 - 114,223 (-)NCBI
UNSW_CanFamBas_1.010354,435 - 357,335 (-)NCBI
UU_Cfam_GSD_1.010478,330 - 481,230 (-)NCBI
Cd63
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,671,044 - 58,674,233 (+)NCBI
SpeTri2.0NW_004936646196,002 - 199,177 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD63
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,171,678 - 21,176,232 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,172,275 - 21,176,225 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2522,652,127 - 22,656,077 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD63
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11151,673,402 - 51,677,075 (-)NCBI
ChlSab1.1 Ensembl1151,672,740 - 51,676,301 (-)Ensembl
Vero_WHO_p1.0NW_023666037194,317,476 - 194,321,231 (+)NCBI
Cd63
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480212,290,733 - 12,294,293 (+)NCBI

Position Markers
RH130054  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,339,842 - 1,340,363 (+)MAPPER
Rnor_6.073,334,979 - 3,335,499NCBIRnor6.0
Rnor_5.073,305,198 - 3,305,718UniSTSRnor5.0
RGSC_v3.472,210,723 - 2,211,243UniSTSRGSC3.4
Celera71,210,649 - 1,211,169UniSTS
Cytogenetic Map7q11UniSTS
RH131837  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,340,720 - 1,340,940 (+)MAPPER
Rnor_6.073,335,857 - 3,336,076NCBIRnor6.0
Rnor_5.073,306,076 - 3,306,295UniSTSRnor5.0
RGSC_v3.472,211,601 - 2,211,820UniSTSRGSC3.4
Celera71,211,527 - 1,211,746UniSTS
Cytogenetic Map7q11UniSTS
RH137352  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,340,062 - 1,340,411 (+)MAPPER
Rnor_6.073,335,199 - 3,335,547NCBIRnor6.0
Rnor_5.073,305,418 - 3,305,766UniSTSRnor5.0
RGSC_v3.472,210,943 - 2,211,291UniSTSRGSC3.4
Celera71,210,869 - 1,211,217UniSTS
Cytogenetic Map7q11UniSTS
RH139213  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,339,091 - 1,339,399 (+)MAPPER
Rnor_6.073,334,228 - 3,334,535NCBIRnor6.0
Rnor_5.073,304,447 - 3,304,754UniSTSRnor5.0
RGSC_v3.472,209,972 - 2,210,279UniSTSRGSC3.4
Celera71,209,898 - 1,210,205UniSTS
Cytogenetic Map7q11UniSTS
RH125938  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.271,339,822 - 1,340,414 (+)MAPPER
Rnor_6.073,334,959 - 3,335,550NCBIRnor6.0
Rnor_5.073,305,178 - 3,305,769UniSTSRnor5.0
RGSC_v3.472,210,703 - 2,211,294UniSTSRGSC3.4
Celera71,210,629 - 1,211,220UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:101
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000010180
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010180   ⟹   ENSRNOP00000010180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl73,332,788 - 3,335,579 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090381   ⟹   ENSRNOP00000071571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl73,320,103 - 3,335,582 (+)Ensembl
RefSeq Acc Id: NM_017125   ⟹   NP_058821
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.271,337,652 - 1,340,443 (+)NCBI
Rnor_6.073,332,788 - 3,335,579 (+)NCBI
Rnor_5.073,303,449 - 3,305,798 (+)NCBI
RGSC_v3.472,208,659 - 2,211,323 (+)RGD
Celera71,208,422 - 1,211,249 (+)RGD
Sequence:
RefSeq Acc Id: XM_008765024   ⟹   XP_008763246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.271,325,108 - 1,340,447 (+)NCBI
Rnor_6.073,320,250 - 3,335,583 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765025   ⟹   XP_008763247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.271,337,598 - 1,340,447 (+)NCBI
Rnor_6.073,332,771 - 3,335,583 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058821   ⟸   NM_017125
- UniProtKB: P28648 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763246   ⟸   XM_008765024
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0T2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763247   ⟸   XM_008765025
- Peptide Label: isoform X2
- UniProtKB: P28648 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071571   ⟸   ENSRNOT00000090381
RefSeq Acc Id: ENSRNOP00000010180   ⟸   ENSRNOT00000010180

Transcriptome

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

Promoters
RGD ID:13694957
Promoter ID:EPDNEW_R5481
Type:initiation region
Name:Cd63_1
Description:Cd63 molecule
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_6.073,332,784 - 3,332,844EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62080 AgrOrtholog
Ensembl Genes ENSRNOG00000007650 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010180 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071571 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010180 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000090381 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.1450.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6921594 IMAGE-MGC_LOAD
InterPro CD63_LEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin/Peripherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin_EC2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29186 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72893 IMAGE-MGC_LOAD
NCBI Gene 29186 ENTREZGENE
Pfam Tetraspanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd63 PhenoGen
PIRSF Tetraspanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS TMFOUR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TM4_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48652 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K0T2 ENTREZGENE, UniProtKB/TrEMBL
  CD63_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-29 Cd63  Cd63 molecule  Cd63  CD63 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Cd63  CD63 antigen      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains four predicted membrane-spanning helices and three potential N-glycosylation sites 61549