Ssc5d (scavenger receptor cysteine rich family member with 5 domains) - Rat Genome Database
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Gene: Ssc5d (scavenger receptor cysteine rich family member with 5 domains) Rattus norvegicus
Analyze
Symbol: Ssc5d
Name: scavenger receptor cysteine rich family member with 5 domains
RGD ID: 1565772
Description: Predicted to have fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in negative regulation of interleukin-8 production and response to bacterium. Predicted to localize to collagen-containing extracellular matrix and extracellular space. Orthologous to human SSC5D (scavenger receptor cysteine rich family member with 5 domains); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hypothetical protein LOC308341; LOC308341; RGD1565772; scavenger receptor cysteine rich domain containing (5 domains); scavenger receptor cysteine rich family, 5 domains; similar to hypothetical protein A430110N23; soluble scavenger receptor cysteine-rich domain-containing protein SSC5D
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
mRatBN7.2168,891,942 - 68,910,462 (-)NCBI
Rnor_6.0 Ensembl172,443,758 - 72,461,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0172,443,750 - 72,462,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0176,073,784 - 76,092,321 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4167,630,584 - 67,648,373 (-)NCBIRGSC3.4rn4RGSC3.4
Celera168,209,472 - 68,227,251 (+)NCBICelera
Cytogenetic Map1q12NCBI
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

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:21217009   PMID:24006456  


Genomics

Comparative Map Data
Ssc5d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2168,891,942 - 68,910,462 (-)NCBI
Rnor_6.0 Ensembl172,443,758 - 72,461,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0172,443,750 - 72,462,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0176,073,784 - 76,092,321 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4167,630,584 - 67,648,373 (-)NCBIRGSC3.4rn4RGSC3.4
Celera168,209,472 - 68,227,251 (+)NCBICelera
Cytogenetic Map1q12NCBI
SSC5D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1955,488,404 - 55,519,099 (+)EnsemblGRCh38hg38GRCh38
GRCh381955,488,436 - 55,519,099 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371955,999,803 - 56,030,466 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361960,691,682 - 60,722,278 (+)NCBINCBI36hg18NCBI36
Celera1953,039,800 - 53,070,315 (+)NCBI
Cytogenetic Map19q13.42NCBI
HuRef1952,312,957 - 52,343,555 (+)NCBIHuRef
CHM1_11955,993,884 - 56,024,489 (+)NCBICHM1_1
Ssc5d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3974,928,820 - 4,947,827 (+)NCBIGRCm39mm39
GRCm39 Ensembl74,928,784 - 4,947,825 (+)Ensembl
GRCm3874,925,129 - 4,944,828 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl74,925,785 - 4,944,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv3774,877,446 - 4,896,399 (+)NCBIGRCm37mm9NCBIm37
MGSCv3674,528,931 - 4,547,884 (+)NCBImm8
Celera74,667,408 - 4,686,397 (+)NCBICelera
Cytogenetic Map7A1NCBI
Ssc5d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955567789,182 - 809,636 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955567789,396 - 809,597 (-)NCBIChiLan1.0ChiLan1.0
SSC5D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11961,220,816 - 61,251,429 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1961,222,371 - 61,251,329 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01952,532,857 - 52,563,244 (+)NCBIMhudiblu_PPA_v0panPan3
SSC5D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1102,196,890 - 102,221,444 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11102,195,426 - 102,222,352 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ssc5d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936886715,159 - 734,428 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSC5D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl659,641,647 - 59,665,331 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1659,641,220 - 59,672,249 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2654,603,844 - 54,608,819 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SSC5D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1648,083,375 - 48,105,356 (+)NCBI
ChlSab1.1 Ensembl648,083,543 - 48,105,218 (+)Ensembl
Ssc5d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248321,849,688 - 1,868,207 (-)NCBI

Position Markers
D1Got360  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0172,446,839 - 72,447,071NCBIRnor6.0
Rnor_5.0176,089,006 - 76,089,238UniSTSRnor5.0
RGSC_v3.4167,633,665 - 67,633,897UniSTSRGSC3.4
Celera168,223,938 - 68,224,170UniSTS
Cytogenetic Map1q12UniSTS
BE097029  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0172,462,800 - 72,462,952NCBIRnor6.0
Rnor_5.0176,073,125 - 76,073,277UniSTSRnor5.0
RGSC_v3.4167,649,626 - 67,649,778UniSTSRGSC3.4
Celera168,208,067 - 68,208,219UniSTS
Cytogenetic Map1q12UniSTS
RH135111  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0172,443,897 - 72,444,107NCBIRnor6.0
Rnor_5.0176,091,970 - 76,092,180UniSTSRnor5.0
RGSC_v3.4167,630,723 - 67,630,933UniSTSRGSC3.4
Celera168,226,902 - 68,227,112UniSTS
Cytogenetic Map1q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)12429779978748000Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13444911279449112Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13444911279449112Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13585416780854167Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13603316579689689Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13603316579689689Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14611346179689689Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14954732883657083Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15385134883657083Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15385134883657083Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:23
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000022480
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 6 1 2 10 28 1
Low 3 37 23 14 9 14 7 9 74 17 11 11 7
Below cutoff 33 26 10 26 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022480   ⟹   ENSRNOP00000022480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl172,443,758 - 72,461,547 (-)Ensembl
RefSeq Acc Id: NM_001134545   ⟹   NP_001128017
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2168,891,949 - 68,909,743 (-)NCBI
Rnor_6.0172,443,758 - 72,461,547 (-)NCBI
Rnor_5.0176,073,784 - 76,092,321 (+)NCBI
RGSC_v3.4167,630,584 - 67,648,373 (-)RGD
Celera168,209,472 - 68,227,251 (+)RGD
Sequence:
RefSeq Acc Id: XM_006228257   ⟹   XP_006228319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2168,891,942 - 68,910,462 (-)NCBI
Rnor_6.0172,443,750 - 72,462,293 (-)NCBI
Rnor_5.0176,073,784 - 76,092,321 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589109   ⟹   XP_017444598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0172,443,750 - 72,461,382 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001128017 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228319 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75875 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001128017   ⟸   NM_001134545
- Peptide Label: precursor
- UniProtKB: D3ZPK4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228319   ⟸   XM_006228257
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444598   ⟸   XM_017589109
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000022480   ⟸   ENSRNOT00000022480
Protein Domains
SRCR

Transcriptome

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

Promoters
RGD ID:13689691
Promoter ID:EPDNEW_R216
Type:initiation region
Name:Ssc5d_1
Description:scavenger receptor cysteine rich family member with 5 domains
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_6.0172,461,560 - 72,461,620EPDNEW

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)
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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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/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
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
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 76083781 76083782 A G snv GH/OmrMcwi (MCW), BUF/MNa (KyushuU), SDLEF7/Barth (UDEL), WN/N (KNAW), M520/N (KNAW), LH/MavRrrc (KNAW)
1 76091216 76091217 T G snv FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), HTX/Kyo (KyushuU), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), FHL/EurMcwi (MCW), DOB/Oda (KyushuU), FHH/EurMcwi (MCW)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 72444861 72444862 A C snv WKY/Gcrc (RGD), WKY/NCrl (RGD), FHH/EurMcwi (MCW), FHH/EurMcwi (RGD), FHL/EurMcwi (MCW), WKY/N (MCW), WKY/NHsd (RGD), FHL/EurMcwi (RGD)
1 72452296 72452297 T C snv LH/MavRrrc (RGD), M520/N (MCW), CDR, GH/OmrMcwi (MCW), WN/N (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 67639122 67639123 T C snv M520/N (KNAW), LH/MavRrrc (ICL), GH/OmrMcwi (MCW), WN/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565772 AgrOrtholog
Ensembl Genes ENSRNOG00000016687 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022480 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022480 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.250.10 UniProtKB/TrEMBL
InterPro SRCR-like_dom_sf UniProtKB/TrEMBL
  Srcr_rcpt UniProtKB/TrEMBL
  Srcr_rcpt-rel UniProtKB/TrEMBL
KEGG Report rno:308341 UniProtKB/TrEMBL
NCBI Gene 308341 ENTREZGENE
Pfam SRCR UniProtKB/TrEMBL
PhenoGen Ssc5d PhenoGen
PRINTS SPERACTRCPTR UniProtKB/TrEMBL
PROSITE SRCR_1 UniProtKB/TrEMBL
  SRCR_2 UniProtKB/TrEMBL
SMART SM00202 UniProtKB/TrEMBL
Superfamily-SCOP Srcr_receptor UniProtKB/TrEMBL
UniProt D3ZPK4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Ssc5d  scavenger receptor cysteine rich family member with 5 domains  Ssc5d  scavenger receptor cysteine rich family, 5 domains  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-07-16 Ssc5d  scavenger receptor cysteine rich family, 5 domains  Ssc5d  scavenger receptor cysteine rich domain containing (5 domains)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-05-25 Ssc5d  scavenger receptor cysteine rich domain containing (5 domains)  RGD1565772  similar to hypothetical protein A430110N23  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565772  similar to hypothetical protein A430110N23   RGD1565772_predicted  similar to hypothetical protein A430110N23 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565772_predicted  similar to hypothetical protein A430110N23 (predicted)  LOC308341  similar to hypothetical protein A430110N23  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC308341  similar to hypothetical protein A430110N23      Symbol and Name status set to provisional 70820 PROVISIONAL