Scarb2 (scavenger receptor class B, member 2) - Rat Genome Database
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Gene: Scarb2 (scavenger receptor class B, member 2) Rattus norvegicus
Analyze
Symbol: Scarb2
Name: scavenger receptor class B, member 2
RGD ID: 621882
Description: Predicted to have several functions, including chaperone binding activity; cholesterol binding activity; and phospholipid binding activity. Involved in positive regulation of neuron projection development. Predicted to localize to endocytic vesicle membrane; lysosome; and plasma membrane. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy 4. Orthologous to human SCARB2 (scavenger receptor class B member 2); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 85 kDa lysosomal membrane sialoglycoprotein; CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2; CD36 antigen-like 2; Cd36l2; LGP85; LIMP II; LimpII; lysosome membrane protein 2; lysosome membrane protein II; scavenger receptor class B member 2
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
mRatBN7.21415,558,271 - 15,609,813 (+)NCBI
Rnor_6.0 Ensembl1417,064,353 - 17,115,963 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01417,064,173 - 17,115,620 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01416,980,270 - 17,031,712 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,119,366 - 17,170,850 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11417,119,365 - 17,170,850 (+)NCBI
Celera1414,952,893 - 15,004,293 (+)NCBICelera
Cytogenetic Map14p22NCBI
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  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
ampicillin  (EXP)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
isoprenaline  (ISO)
L-methionine  (ISO)
leflunomide  (EXP,ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
metronidazole  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
neomycin  (EXP)
nimesulide  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
pirinixic acid  (EXP,ISO)
rotenone  (ISO)
sarin  (ISO)
sirolimus  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tauroursodeoxycholic acid  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloroethene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (EXP)
Yessotoxin  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:1859403   PMID:15489334   PMID:16138903   PMID:17897319   PMID:18022370   PMID:19056867   PMID:19946888   PMID:21423176   PMID:23376485   PMID:23533145   PMID:25202012   PMID:25316793  
PMID:27789271   PMID:29199275   PMID:32007273  


Genomics

Comparative Map Data
Scarb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21415,558,271 - 15,609,813 (+)NCBI
Rnor_6.0 Ensembl1417,064,353 - 17,115,963 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01417,064,173 - 17,115,620 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01416,980,270 - 17,031,712 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,119,366 - 17,170,850 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11417,119,365 - 17,170,850 (+)NCBI
Celera1414,952,893 - 15,004,293 (+)NCBICelera
Cytogenetic Map14p22NCBI
SCARB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl476,158,737 - 76,234,536 (-)EnsemblGRCh38hg38GRCh38
GRCh38476,158,737 - 76,213,824 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37477,079,890 - 77,134,977 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36477,298,918 - 77,354,059 (-)NCBINCBI36hg18NCBI36
Build 34477,437,072 - 77,492,214NCBI
Celera474,380,030 - 74,435,161 (-)NCBI
Cytogenetic Map4q21.1NCBI
HuRef472,831,916 - 72,887,070 (-)NCBIHuRef
CHM1_1477,056,276 - 77,111,407 (-)NCBICHM1_1
Scarb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,589,170 - 92,653,516 (-)NCBIGRCm39mm39
GRCm39 Ensembl592,589,173 - 92,654,692 (-)Ensembl
GRCm38592,441,311 - 92,505,657 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl592,441,314 - 92,506,833 (-)EnsemblGRCm38mm10GRCm38
MGSCv37592,872,899 - 92,934,634 (-)NCBIGRCm37mm9NCBIm37
MGSCv36593,519,073 - 93,580,808 (-)NCBImm8
Celera590,592,338 - 90,656,687 (-)NCBICelera
Cytogenetic Map5E2NCBI
Scarb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955433884,740 - 962,932 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955433884,740 - 962,932 (-)NCBIChiLan1.0ChiLan1.0
SCARB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1453,830,488 - 53,886,065 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl453,830,488 - 53,886,059 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0447,992,589 - 48,047,528 (+)NCBIMhudiblu_PPA_v0panPan3
SCARB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.132788,117 - 865,496 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl32790,379 - 865,502 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3241,016,853 - 41,094,397 (+)NCBI
ROS_Cfam_1.032814,945 - 891,722 (-)NCBI
UMICH_Zoey_3.132812,765 - 889,655 (-)NCBI
UNSW_CanFamBas_1.032767,039 - 843,700 (-)NCBI
UU_Cfam_GSD_1.03239,325,616 - 39,402,476 (+)NCBI
Scarb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_02440528511,281,403 - 11,339,761 (+)NCBI
SpeTri2.0NW_004936676167,482 - 225,827 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCARB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl871,838,788 - 71,940,607 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1871,838,395 - 71,910,461 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2876,034,114 - 76,105,880 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCARB2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1724,658,734 - 24,714,631 (-)NCBI
ChlSab1.1 Ensembl724,658,211 - 24,714,597 (-)Ensembl
Scarb2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475714,709,120 - 14,795,039 (+)NCBI

Position Markers
D14Got18  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01417,065,890 - 17,066,060NCBIRnor6.0
Rnor_5.01416,981,987 - 16,982,157UniSTSRnor5.0
RGSC_v3.41417,121,082 - 17,121,253RGDRGSC3.4
RGSC_v3.41417,121,083 - 17,121,253UniSTSRGSC3.4
RGSC_v3.11417,121,083 - 17,121,253RGD
Celera1414,954,610 - 14,954,780UniSTS
RH 3.4 Map14190.0RGD
RH 3.4 Map14190.0UniSTS
RH 2.0 Map14203.0RGD
Cytogenetic Map14p22UniSTS
D14Got20  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01417,094,964 - 17,095,141NCBIRnor6.0
Rnor_5.01417,011,056 - 17,011,233UniSTSRnor5.0
RGSC_v3.41417,150,193 - 17,150,371RGDRGSC3.4
RGSC_v3.41417,150,194 - 17,150,371UniSTSRGSC3.4
RGSC_v3.11417,150,193 - 17,150,371RGD
Celera1414,983,663 - 14,983,840UniSTS
RH 2.0 Map14206.9RGD
Cytogenetic Map14p22UniSTS
BM390590  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01417,103,653 - 17,103,866NCBIRnor6.0
Rnor_5.01417,019,745 - 17,019,958UniSTSRnor5.0
RGSC_v3.41417,158,883 - 17,159,096UniSTSRGSC3.4
Celera1414,992,326 - 14,992,539UniSTS
RH 3.4 Map14213.1UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:32
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000003052
Prediction methods: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 42 57 41 19 41 8 11 74 35 36 11 8
Low 1 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003052   ⟹   ENSRNOP00000003052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1417,064,353 - 17,115,963 (+)Ensembl
RefSeq Acc Id: NM_054001   ⟹   NP_446453
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21415,558,271 - 15,609,813 (+)NCBI
Rnor_6.01417,064,173 - 17,115,620 (+)NCBI
Rnor_5.01416,980,270 - 17,031,712 (+)NCBI
RGSC_v3.41417,119,366 - 17,170,850 (+)RGD
Celera1414,952,893 - 15,004,293 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446453   ⟸   NM_054001
- Peptide Label: precursor
- UniProtKB: P27615 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003052   ⟸   ENSRNOT00000003052

Transcriptome

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


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)
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
LN/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
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:621882 AgrOrtholog
Ensembl Genes ENSRNOG00000002225 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003052 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003052 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621697 IMAGE-MGC_LOAD
InterPro CD36/SCARB1/SNMP1 UniProtKB/TrEMBL
  CD36_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LimpII UniProtKB/Swiss-Prot
KEGG Report rno:117106 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72341 IMAGE-MGC_LOAD
NCBI Gene 117106 ENTREZGENE
PANTHER PTHR11923 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CD36 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scarb2 PhenoGen
PRINTS CD36ANTIGEN UniProtKB/TrEMBL
  CD36FAMILY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIMPII UniProtKB/Swiss-Prot
UniProt P27615 ENTREZGENE
  Q6B4I7_RAT UniProtKB/TrEMBL
  SCRB2_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Scarb2  scavenger receptor class B, member 2    CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2  Name updated 1299863 APPROVED
2004-09-10 Scarb2  CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2  Cd36l2    Symbol and Name updated 1299863 APPROVED
2002-08-07 Cd36l2  CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology has a high degree of homology to cell adhesion protein CD36 632394
gene_protein consists of 478 amino acid residues and has 11 potential N-glycosylation sites and 5 cysteine residues 632394