Scara5 (scavenger receptor class A, member 5) - Rat Genome Database
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Gene: Scara5 (scavenger receptor class A, member 5) Rattus norvegicus
Analyze
Symbol: Scara5
Name: scavenger receptor class A, member 5
RGD ID: 1306539
Description: Predicted to have ferritin receptor activity. Predicted to be involved in several processes, including cellular iron ion homeostasis; cellular response to heat; and protein homotrimerization. Predicted to localize to external side of plasma membrane and integral component of plasma membrane. Orthologous to human SCARA5 (scavenger receptor class A member 5); INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; acrylamide; atrazine.
Type: protein-coding
RefSeq Status: INFERRED
Also known as: LOC305974; RGD1306539; scavenger receptor class A member 5; scavenger receptor class A, member 5 (putative); similar to RIKEN cDNA 4933425F03
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
Rnor_6.01549,069,142 - 49,177,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,069,145 - 49,177,166 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01552,807,988 - 52,912,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,083,644 - 45,189,211 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11545,112,218 - 45,202,970 (+)NCBI
Celera1539,553,541 - 39,658,427 (+)NCBICelera
Cytogenetic Map15p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:16407294   PMID:18755693   PMID:19154717   PMID:21810271  


Genomics

Comparative Map Data
Scara5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01549,069,142 - 49,177,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,069,145 - 49,177,166 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01552,807,988 - 52,912,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,083,644 - 45,189,211 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11545,112,218 - 45,202,970 (+)NCBI
Celera1539,553,541 - 39,658,427 (+)NCBICelera
Cytogenetic Map15p11NCBI
SCARA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl827,869,883 - 27,992,673 (-)EnsemblGRCh38hg38GRCh38
GRCh38827,869,883 - 27,992,673 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37827,727,399 - 27,850,369 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36827,783,655 - 27,906,117 (-)NCBINCBI36hg18NCBI36
Celera826,687,547 - 26,810,041 (-)NCBI
Cytogenetic Map8p21.1NCBI
HuRef826,272,203 - 26,395,878 (-)NCBIHuRef
CHM1_1827,929,218 - 28,052,486 (-)NCBICHM1_1
Scara5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391465,903,852 - 66,002,275 (+)NCBIGRCm39mm39
GRCm381465,666,403 - 65,764,826 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1465,666,403 - 65,764,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv371466,285,240 - 66,383,663 (+)NCBIGRCm37mm9NCBIm37
MGSCv361464,620,537 - 64,718,936 (+)NCBImm8
Celera1463,417,881 - 63,517,650 (+)NCBICelera
Cytogenetic Map14D1NCBI
Scara5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540350,386,125 - 50,486,361 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540350,386,212 - 50,486,335 (-)NCBIChiLan1.0ChiLan1.0
SCARA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1824,345,260 - 24,469,881 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl824,345,260 - 24,469,881 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0827,143,737 - 27,271,301 (-)NCBIMhudiblu_PPA_v0panPan3
SCARA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2529,591,294 - 29,712,173 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12529,591,248 - 29,714,159 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Scara5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936675763,467 - 868,021 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCARA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11411,615,629 - 11,747,336 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21412,845,888 - 12,978,031 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCARA5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1825,975,310 - 26,097,312 (-)NCBI
ChlSab1.1 Ensembl825,975,122 - 26,097,102 (-)Ensembl
Scara5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475822,661,136 - 22,757,578 (-)NCBI

Position Markers
D15Rat120  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,111,041 - 49,111,151NCBIRnor6.0
Rnor_5.01552,847,018 - 52,847,128UniSTSRnor5.0
RGSC_v3.41545,124,534 - 45,124,641RGDRGSC3.4
RGSC_v3.41545,124,531 - 45,124,641UniSTSRGSC3.4
RGSC_v3.11545,140,234 - 45,140,341RGD
Celera1539,592,707 - 39,592,817UniSTS
Cytogenetic Map15p12UniSTS
SHRSP x BN Map1533.4699UniSTS
SHRSP x BN Map1533.4699RGD
D15Rat143  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,081,619 - 49,081,759NCBIRnor6.0
Rnor_5.01552,817,596 - 52,817,736UniSTSRnor5.0
RGSC_v3.41545,094,621 - 45,094,762RGDRGSC3.4
RGSC_v3.41545,094,622 - 45,094,762UniSTSRGSC3.4
RGSC_v3.11545,110,321 - 45,110,462RGD
Celera1539,563,249 - 39,563,391UniSTS
Cytogenetic Map15p12UniSTS
RH 2.0 Map15275.0RGD
SHRSP x BN Map1533.4699RGD
D15Got47  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,110,979 - 49,111,138NCBIRnor6.0
Rnor_5.01552,846,956 - 52,847,115UniSTSRnor5.0
RGSC_v3.41545,124,468 - 45,124,628RGDRGSC3.4
RGSC_v3.41545,124,469 - 45,124,628UniSTSRGSC3.4
RGSC_v3.11545,140,168 - 45,140,328RGD
Celera1539,592,645 - 39,592,804UniSTS
Cytogenetic Map15p12UniSTS
RH 2.0 Map15277.2RGD
30.MMHAP14FRB12.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,168,397 - 49,168,504NCBIRnor6.0
Rnor_5.01552,903,726 - 52,903,833UniSTSRnor5.0
RGSC_v3.41545,180,449 - 45,180,556UniSTSRGSC3.4
Celera1539,649,665 - 39,649,772UniSTS
Cytogenetic Map15p12UniSTS
RH139634  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,176,790 - 49,176,969NCBIRnor6.0
Rnor_5.01552,912,119 - 52,912,298UniSTSRnor5.0
RGSC_v3.41545,188,842 - 45,189,021UniSTSRGSC3.4
Celera1539,658,058 - 39,658,237UniSTS
Cytogenetic Map15p12UniSTS
RH138852  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,158,965 - 49,159,179NCBIRnor6.0
Rnor_5.01552,894,294 - 52,894,508UniSTSRnor5.0
RGSC_v3.41545,171,017 - 45,171,231UniSTSRGSC3.4
Celera1539,640,233 - 39,640,447UniSTS
Cytogenetic Map15p12UniSTS
UniSTS:478958  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01549,143,000 - 49,143,302NCBIRnor6.0
Rnor_5.01552,878,170 - 52,878,472UniSTSRnor5.0
RGSC_v3.41545,155,083 - 45,155,385UniSTSRGSC3.4
Celera1539,624,290 - 39,624,592UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154309747052831189Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:61
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000019487
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 9 1 12 23 4
Low 2 26 25 10 7 10 8 11 66 34 15 7 8
Below cutoff 1 6 31 31 31 8 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019487   ⟹   ENSRNOP00000019487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1549,069,145 - 49,177,166 (+)Ensembl
RefSeq Acc Id: NM_001135855   ⟹   NP_001129327
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01549,069,180 - 49,177,159 (+)NCBI
Rnor_5.01552,807,988 - 52,912,488 (+)NCBI
RGSC_v3.41545,083,644 - 45,189,211 (+)RGD
Celera1539,553,541 - 39,658,427 (+)RGD
Sequence:
RefSeq Acc Id: XM_006252204   ⟹   XP_006252266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01549,069,142 - 49,177,158 (+)NCBI
Rnor_5.01552,807,988 - 52,912,488 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129327 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252266 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85362 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001129327   ⟸   NM_001135855
- Sequence:
RefSeq Acc Id: XP_006252266   ⟸   XM_006252204
- Peptide Label: isoform X1
- UniProtKB: D4A213 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019487   ⟸   ENSRNOT00000019487
Protein Domains
SRCR

Transcriptome

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

Promoters
RGD ID:13699790
Promoter ID:EPDNEW_R10313
Type:initiation region
Name:Scara5_1
Description:scavenger receptor class A, member 5
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_6.01549,069,161 - 49,069,221EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 52878505 52878506 C T snv GH/OmrMcwi (MCW), SBN/Ygl (MCW), BBDP/WorN (KNAW), SBN/Ygl (KNAW), LEC/Tj (KyushuU), LE/Stm (SOLiD) (KNAW), HTX/Kyo (KyushuU), HWY/Slc (KyushuU), LE/Stm (Illumina) (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 49143335 49143336 C T snv GH/OmrMcwi (MCW), SBN/Ygl (MCW), SBN/Ygl (RGD), BBDP/Wor (RGD), LE/Stm (RGD), CDR


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 45155418 45155419 C T snv GH/OmrMcwi (MCW), SBN/Ygl (ICL), LE/Stm (ICL), BBDP/WorN (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306539 AgrOrtholog
Ensembl Genes ENSRNOG00000014398 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019487 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019487 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.250.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  SCARA5 UniProtKB/TrEMBL
  SRCR-like_dom_sf UniProtKB/TrEMBL
  Srcr_rcpt UniProtKB/TrEMBL
  Srcr_rcpt-rel UniProtKB/TrEMBL
NCBI Gene 305974 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  SRCR UniProtKB/TrEMBL
PhenoGen Scara5 PhenoGen
PRINTS SPERACTRCPTR UniProtKB/TrEMBL
PROSITE SRCR_1 UniProtKB/TrEMBL
  SRCR_2 UniProtKB/TrEMBL
SMART SM00202 UniProtKB/TrEMBL
Superfamily-SCOP Srcr_receptor UniProtKB/TrEMBL
UniGene Rn.163284 ENTREZGENE
UniProt D4A213 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary D3Z926 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-16 Scara5  scavenger receptor class A, member 5  Scara5  scavenger receptor class A, member 5 (putative)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Scara5  scavenger receptor class A, member 5 (putative)   Scara5_predicted  scavenger receptor class A, member 5 (putative) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Scara5_predicted  scavenger receptor class A, member 5 (putative) (predicted)  RGD1306539_predicted  similar to RIKEN cDNA 4933425F03 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306539_predicted  similar to RIKEN cDNA 4933425F03 (predicted)  LOC305974_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305974_predicted  similar to RIKEN cDNA 4933425F03 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL