Msr1 (macrophage scavenger receptor 1) - Rat Genome Database
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Gene: Msr1 (macrophage scavenger receptor 1) Rattus norvegicus
Analyze
Symbol: Msr1
Name: macrophage scavenger receptor 1
RGD ID: 1564316
Description: Predicted to have amyloid-beta binding activity; cargo receptor activity; and low-density lipoprotein particle binding activity. Involved in cellular response to organic cyclic compound. Localizes to cytoplasmic vesicle; cytosol; and plasma membrane. Human ortholog(s) of this gene implicated in Barrett's esophagus; arteriosclerosis; and prostate cancer. Orthologous to human MSR1 (macrophage scavenger receptor 1); PARTICIPATES IN phagocytosis pathway; INTERACTS WITH 1,2-dimethylhydrazine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC498638; macrophage scavenger receptor types I and II; RGD1564316; similar to scavenger receptor type A SR-A
Orthologs:
Homo sapiens (human) : MSR1 (macrophage scavenger receptor 1)  HGNC  Alliance
Mus musculus (house mouse) : Msr1 (macrophage scavenger receptor 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Msr1 (macrophage scavenger receptor 1)
Pan paniscus (bonobo/pygmy chimpanzee) : MSR1 (macrophage scavenger receptor 1)
Canis lupus familiaris (dog) : MSR1 (macrophage scavenger receptor 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Msr1 (macrophage scavenger receptor 1)
Sus scrofa (pig) : MSR1 (macrophage scavenger receptor 1)
Chlorocebus sabaeus (African green monkey) : MSR1 (macrophage scavenger receptor 1)
Heterocephalus glaber (naked mole-rat) : Msr1 (macrophage scavenger receptor 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01656,817,714 - 56,900,025 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1656,813,791 - 56,900,052 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01656,516,982 - 56,597,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41656,278,223 - 56,345,472 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1650,621,592 - 50,686,791 (+)NCBICelera
Cytogenetic Map16q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-lipoic acid  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
antirheumatic drug  (ISO)
apocynin  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
cholesterol  (ISO)
choline  (ISO)
chrysene  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
demethoxycurcumin  (ISO)
desferrioxamine B  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furosemide  (EXP)
glyphosate  (EXP)
hydrogen peroxide  (ISO)
hydroxyl  (ISO)
irinotecan  (EXP)
isoprenaline  (ISO)
L-methionine  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
mercury atom  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
methyl methanesulfonate  (ISO)
miquelianin  (ISO)
Monobutylphthalate  (EXP)
paracetamol  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
procyanidin B3  (ISO)
quartz  (EXP)
resveratrol  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium benzoate  (ISO)
tamibarotene  (ISO)
Tanshinone I  (ISO)
TEMPO  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
zinc oxide  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11240025   PMID:12376530   PMID:17148552   PMID:17237231   PMID:21765240   PMID:22438044   PMID:23823020   PMID:24718459  


Genomics

Comparative Map Data
Msr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01656,817,714 - 56,900,025 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1656,813,791 - 56,900,052 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01656,516,982 - 56,597,180 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41656,278,223 - 56,345,472 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1650,621,592 - 50,686,791 (+)NCBICelera
Cytogenetic Map16q12.1NCBI
MSR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl816,107,878 - 16,567,490 (-)EnsemblGRCh38hg38GRCh38
GRCh38816,107,881 - 16,192,651 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37815,965,387 - 16,050,300 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36816,009,758 - 16,094,671 (-)NCBINCBI36hg18NCBI36
Build 34816,009,760 - 16,094,595NCBI
Celera814,929,936 - 15,014,828 (-)NCBI
Cytogenetic Map8p22NCBI
HuRef814,509,923 - 14,594,638 (-)NCBIHuRef
CHM1_1816,167,312 - 16,251,899 (-)NCBICHM1_1
Msr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39839,996,284 - 40,095,790 (-)NCBI
GRCm38839,543,232 - 39,642,750 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl839,581,685 - 39,642,673 (-)EnsemblGRCm38mm10GRCm38
MGSCv37840,667,054 - 40,728,032 (-)NCBIGRCm37mm9NCBIm37
MGSCv36841,102,269 - 41,141,495 (-)NCBImm8
Celera842,254,529 - 42,315,500 (-)NCBICelera
Cytogenetic Map8A4NCBI
cM Map823.89NCBI
Msr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554631,197,022 - 1,264,765 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554631,197,086 - 1,263,943 (+)NCBIChiLan1.0ChiLan1.0
MSR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1812,091,543 - 12,175,927 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl812,088,873 - 12,175,927 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0815,335,795 - 15,421,472 (-)NCBIMhudiblu_PPA_v0panPan3
MSR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1639,436,753 - 39,527,438 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11639,434,948 - 39,513,727 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Msr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365735,345,282 - 5,391,946 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl173,857,171 - 3,939,726 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1173,859,903 - 3,939,612 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2174,110,409 - 4,191,629 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSR1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl814,220,529 - 14,304,946 (-)Ensembl
ChlSab1.1814,221,389 - 14,305,059 (-)NCBI
Msr1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624839694,149 - 769,322 (+)NCBI

Position Markers
L04275  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01656,855,484 - 56,855,626NCBIRnor6.0
Rnor_5.01656,554,428 - 56,554,570UniSTSRnor5.0
RGSC_v3.41656,307,067 - 56,307,209UniSTSRGSC3.4
Celera1650,649,092 - 50,649,234UniSTS
Cytogenetic Map16q12.1UniSTS
RH127715  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1650,678,418 - 50,678,630UniSTS
Celera5164,343,501 - 164,343,713UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map16q12.1UniSTS
AA900898  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera5164,342,363 - 164,342,551UniSTS
Celera1650,677,236 - 50,677,425UniSTS
Cytogenetic Map1p11UniSTS
Cytogenetic Map16q12.1UniSTS
Cytogenetic Map5q36UniSTS
RH 3.4 Map8849.9UniSTS
UniSTS:496680  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.02176,377,830 - 176,378,105NCBIRnor5.0
Rnor_5.03151,876,035 - 151,876,320NCBIRnor5.0
Rnor_5.01656,527,453 - 56,527,738NCBIRnor5.0
RGSC_v3.4132,051,429 - 32,051,703UniSTSRGSC3.4
RGSC_v3.41656,334,152 - 56,334,436UniSTSRGSC3.4
Celera1650,676,178 - 50,676,462UniSTS
Cytogenetic Map16q12.1UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162484654169846541Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162751998072519980Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162834031573340315Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163530711063909364Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:22
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000017339
Prediction methods:Miranda, Rnahybrid
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 8 8 9 8 2
Low 2 30 49 33 10 33 8 8 8 33 31 9 8
Below cutoff 1 7 2 64 2 10

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017339   ⟹   ENSRNOP00000017339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1656,813,791 - 56,900,052 (-)Ensembl
RefSeq Acc Id: NM_001191939   ⟹   NP_001178868
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01656,818,085 - 56,885,064 (-)NCBI
Rnor_5.01656,516,982 - 56,597,180 (-)NCBI
Celera1650,621,592 - 50,686,791 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253206   ⟹   XP_006253268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01656,817,714 - 56,900,025 (-)NCBI
Rnor_5.01656,516,982 - 56,597,180 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253207   ⟹   XP_006253269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01656,852,696 - 56,900,019 (-)NCBI
Rnor_5.01656,516,982 - 56,597,180 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178868 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253268 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253269 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78809 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178868   ⟸   NM_001191939
- Sequence:
RefSeq Acc Id: XP_006253268   ⟸   XM_006253206
- Peptide Label: isoform X1
- UniProtKB: D3ZDS2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253269   ⟸   XM_006253207
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000017339   ⟸   ENSRNOT00000017339
Protein Domains
SRCR

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)
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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:1564316 AgrOrtholog
Ensembl Genes ENSRNOG00000012779 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017339 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017339 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.250.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Macro_scav_rcpt UniProtKB/TrEMBL
  SRCR-like_dom_sf UniProtKB/TrEMBL
  Srcr_rcpt UniProtKB/TrEMBL
  Srcr_rcpt-rel UniProtKB/TrEMBL
NCBI Gene 498638 ENTREZGENE
PANTHER PTHR19331:SF440 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  Macscav_rec UniProtKB/TrEMBL
  SRCR UniProtKB/TrEMBL
PhenoGen Msr1 PhenoGen
PRINTS MACSCAVRCPTR UniProtKB/TrEMBL
  SPERACTRCPTR UniProtKB/TrEMBL
PROSITE SRCR_1 UniProtKB/TrEMBL
  SRCR_2 UniProtKB/TrEMBL
SMART SM00202 UniProtKB/TrEMBL
Superfamily-SCOP Srcr_receptor UniProtKB/TrEMBL
UniGene Rn.231068 ENTREZGENE
UniProt D3ZDS2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Msr1  macrophage scavenger receptor 1  RGD1564316_predicted  similar to scavenger receptor type A SR-A (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564316_predicted  similar to scavenger receptor type A SR-A (predicted)  LOC498638  similar to scavenger receptor type A SR-A  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498638  similar to scavenger receptor type A SR-A      Symbol and Name status set to provisional 70820 PROVISIONAL