Sorcs2 (sortilin-related VPS10 domain containing receptor 2) - Rat Genome Database
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Gene: Sorcs2 (sortilin-related VPS10 domain containing receptor 2) Rattus norvegicus
Analyze
Symbol: Sorcs2
Name: sortilin-related VPS10 domain containing receptor 2
RGD ID: 1310621
Description: Predicted to be involved in intracellular protein transport and long-term synaptic depression. Predicted to localize to endosome membrane; integral component of plasma membrane; and postsynaptic density. Orthologous to human SORCS2 (sortilin related VPS10 domain containing receptor 2); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 3,7-dihydropurine-6-thione; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC305438; VPS10 domain receptor protein SORCS 2; VPS10 domain-containing receptor SorCS2
Orthologs:
Allele / Splice: Sorcs2em4Mcwi   Sorcs2em1Mcwi   Sorcs2em7Mcwi   Sorcs2em9Mcwi  
Genetic Models: SS-Sorcs2em4Mcwi SS-Sorcs2em9Mcwi SS-Sorcs2em7Mcwi SS-Sorcs2em1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01479,538,911 - 79,912,333 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1479,538,911 - 79,912,333 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01479,176,694 - 79,547,823 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41479,968,072 - 80,344,330 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11480,096,523 - 80,344,581 (+)NCBI
Celera1473,307,871 - 73,668,512 (+)NCBICelera
Cytogenetic Map14q21NCBI
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:27457814   PMID:30840898  


Genomics

Comparative Map Data
Sorcs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01479,538,911 - 79,912,333 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1479,538,911 - 79,912,333 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01479,176,694 - 79,547,823 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41479,968,072 - 80,344,330 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11480,096,523 - 80,344,581 (+)NCBI
Celera1473,307,871 - 73,668,512 (+)NCBICelera
Cytogenetic Map14q21NCBI
SORCS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl47,192,538 - 7,742,836 (+)EnsemblGRCh38hg38GRCh38
GRCh3847,192,538 - 7,742,828 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3747,194,374 - 7,744,564 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3647,245,373 - 7,795,464 (+)NCBINCBI36hg18NCBI36
Build 3447,312,543 - 7,862,634NCBI
Celera47,098,892 - 7,646,499 (+)NCBI
Cytogenetic Map4p16.1NCBI
HuRef47,121,365 - 7,666,825 (+)NCBIHuRef
CHM1_147,192,978 - 7,742,776 (+)NCBICHM1_1
Sorcs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39536,174,524 - 36,555,541 (-)NCBI
GRCm38536,017,180 - 36,398,197 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl536,017,180 - 36,398,139 (-)EnsemblGRCm38mm10GRCm38
MGSCv37536,359,829 - 36,740,788 (-)NCBIGRCm37mm9NCBIm37
MGSCv36536,334,092 - 36,715,203 (-)NCBImm8
Celera533,494,787 - 33,878,421 (-)NCBICelera
Cytogenetic Map5B3NCBI
Sorcs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555143,053,071 - 3,390,125 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555143,053,127 - 3,390,125 (-)NCBIChiLan1.0ChiLan1.0
SORCS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.147,259,342 - 7,805,275 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl47,259,337 - 7,803,594 (+)Ensemblpanpan1.1panPan2
SORCS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl359,255,848 - 59,679,049 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1359,319,707 - 59,679,071 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sorcs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647718,952,965 - 19,279,053 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SORCS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl83,207,098 - 3,760,393 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.183,207,087 - 3,715,002 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.283,962,102 - 4,004,672 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SORCS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12743,629,273 - 43,700,888 (+)NCBI
Sorcs2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475523,346,247 - 23,657,637 (+)NCBI

Position Markers
D14Rat127  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01479,596,105 - 79,596,334NCBIRnor6.0
Rnor_5.01479,233,168 - 79,233,397UniSTSRnor5.0
RGSC_v3.41480,026,543 - 80,026,772UniSTSRGSC3.4
RGSC_v3.41480,026,542 - 80,026,772RGDRGSC3.4
RGSC_v3.11480,028,934 - 80,029,163RGD
Celera1473,363,714 - 73,363,943UniSTS
Cytogenetic Map14q21UniSTS
RH 3.4 Map14452.44RGD
RH 3.4 Map14452.44UniSTS
SHRSP x BN Map1440.7199RGD
SHRSP x BN Map1440.7199UniSTS
D14Got140  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01479,851,270 - 79,851,468NCBIRnor6.0
Rnor_5.01479,486,998 - 79,487,196UniSTSRnor5.0
RGSC_v3.41480,281,544 - 80,281,742UniSTSRGSC3.4
Cytogenetic Map14q21UniSTS
RH144526  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01479,711,867 - 79,712,078NCBIRnor6.0
Rnor_5.01479,348,058 - 79,348,269UniSTSRnor5.0
RGSC_v3.41480,141,917 - 80,142,128UniSTSRGSC3.4
Celera1473,479,865 - 73,480,076UniSTS
Cytogenetic Map14q21UniSTS
UniSTS:478869  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01479,688,704 - 79,688,851NCBIRnor6.0
Rnor_5.01479,325,231 - 79,325,378UniSTSRnor5.0
RGSC_v3.41480,117,357 - 80,117,504UniSTSRGSC3.4
Celera1473,457,010 - 73,457,157UniSTS
Cytogenetic Map14q21UniSTS
UniSTS:478870  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01479,670,072 - 79,670,214NCBIRnor6.0
Rnor_5.01479,306,599 - 79,306,741UniSTSRnor5.0
RGSC_v3.41480,098,752 - 80,098,894UniSTSRGSC3.4
Celera1473,438,421 - 73,438,555UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat


Genetic Models
This gene Sorcs2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:939
Count of miRNA genes:310
Interacting mature miRNAs:378
Transcripts:ENSRNOT00000009960
Prediction methods:Microtar, Miranda
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 1 18 68 3 24 11
Low 2 24 46 30 19 30 6 8 6 32 17 6
Below cutoff 1 11 11 11 2 3 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07015838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009960   ⟹   ENSRNOP00000009960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1479,538,911 - 79,912,333 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089334   ⟹   ENSRNOP00000074805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1479,540,235 - 79,912,290 (+)Ensembl
RefSeq Acc Id: NM_001107225   ⟹   NP_001100695
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01479,538,911 - 79,912,333 (+)NCBI
Rnor_5.01479,176,694 - 79,547,823 (+)NCBI
RGSC_v3.41479,968,072 - 80,344,330 (+)RGD
Celera1473,307,871 - 73,668,512 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100695 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00049 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100695   ⟸   NM_001107225
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000074805   ⟸   ENSRNOT00000089334
RefSeq Acc Id: ENSRNOP00000009960   ⟸   ENSRNOT00000009960
Protein Domains
PKD

Transcriptome

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

Promoters
RGD ID:13699385
Promoter ID:EPDNEW_R9910
Type:single initiation site
Name:Sorcs2_1
Description:sortilin-related VPS10 domain containing receptor 2
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_6.01479,538,911 - 79,538,971EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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
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
14 79350286 79350287 C T snv ACI/EurMcwi (MCW), ZF (KyushuU), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), DA/BklArbNsi (KNAW), GK/Ox (KNAW), MNS/Gib (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), HWY/Slc (KyushuU), KFRS3B/Kyo (KyushuU), GH/OmrMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 79714095 79714096 C T snv ACI/EurMcwi (MCW), WAG/Rij (RGD), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), MR/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), GK/Ox (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 79968230 79968231 C T snv SHR/OlaIpcv (ICL), DA/BklArbNsi (ICAHN), SS/JrHsdMcwi (MDC), ACI/N (KNAW), MR/N (KNAW), WN/N (KNAW), ACI/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), LE/Stm (ICL), GK/Ox (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310621 AgrOrtholog
Ensembl Genes ENSRNOG00000007033 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009960 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074805 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009960 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089334 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_fold UniProtKB/TrEMBL
  PKD_dom UniProtKB/TrEMBL
  PKD_dom_sf UniProtKB/TrEMBL
  Sortilin_C UniProtKB/TrEMBL
  Sortilin_N UniProtKB/TrEMBL
  VPS10 UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
NCBI Gene 305438 ENTREZGENE
Pfam PKD UniProtKB/TrEMBL
  Sortilin-Vps10 UniProtKB/TrEMBL
  Sortilin_C UniProtKB/TrEMBL
PhenoGen Sorcs2 PhenoGen
PROSITE PKD UniProtKB/TrEMBL
SMART VPS10 UniProtKB/TrEMBL
Superfamily-SCOP PKD UniProtKB/TrEMBL
UniGene Rn.41133 ENTREZGENE
UniProt A0A0G2K902_RAT UniProtKB/TrEMBL
  D3ZW09_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Sorcs2  sortilin-related VPS10 domain containing receptor 2   Sorcs2_predicted  sortilin-related VPS10 domain containing receptor 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sorcs2_predicted  sortilin-related VPS10 domain containing receptor 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED