Vcan (versican) - Rat Genome Database
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Gene: Vcan (versican) Rattus norvegicus
Analyze
Symbol: Vcan
Name: versican
RGD ID: 619940
Description: Predicted to have protein phosphatase binding activity. Involved in axon regeneration. Localizes to cell surface; perineuronal net; and synapse. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in intracranial aneurysm. Orthologous to human VCAN (versican); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: chondroitin sulfate proteoglycan 2; chondroitin sulfate proteoglycan 2 (versican); chondroitin sulfate proteoglycan core protein 2; Cspg2; GHAP; glial hyaluronate-binding protein; large fibroblast proteoglycan; PG-M; versican core protein
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
mRatBN7.2220,761,718 - 20,860,637 (-)NCBI
Rnor_6.0 Ensembl218,490,102 - 18,565,842 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0218,490,102 - 18,587,340 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0218,363,890 - 18,463,115 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4219,712,629 - 19,801,443 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1219,634,740 - 19,688,742 (-)NCBI
Celera216,903,548 - 17,002,158 (-)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsenite(3-)  (ISO)
astemizole  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbofuran  (EXP)
carbon nanotube  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
curcumin  (ISO)
cyclosporin A  (EXP,ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dimethylarsinous acid  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dopamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (ISO)
etoposide  (ISO)
fenoldopam  (EXP)
fenvalerate  (EXP)
furan  (EXP)
hexadecanoic acid  (ISO)
indometacin  (ISO)
isoprenaline  (EXP)
isotretinoin  (ISO)
ketamine  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
mitoxantrone  (ISO)
monosodium L-glutamate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
oleic acid  (ISO)
oxaliplatin  (EXP)
paclitaxel  (EXP)
paracetamol  (ISO)
phenylephrine  (EXP)
phenytoin  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (EXP,ISO)
rofecoxib  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tacrolimus hydrate  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9434070   PMID:9758703   PMID:12701107   PMID:14620382   PMID:15464361   PMID:15668231   PMID:16187070   PMID:16200461   PMID:16210410   PMID:16510873   PMID:16545622   PMID:16648628  
PMID:17972319   PMID:18431253   PMID:18616564   PMID:19437549   PMID:20489207   PMID:20551380   PMID:21976490   PMID:23658023   PMID:24006456   PMID:24719328   PMID:25845936   PMID:26152723  
PMID:26395512   PMID:27068509   PMID:27559042   PMID:29476059   PMID:31429356  


Genomics

Comparative Map Data
Vcan
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2220,761,718 - 20,860,637 (-)NCBI
Rnor_6.0 Ensembl218,490,102 - 18,565,842 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0218,490,102 - 18,587,340 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0218,363,890 - 18,463,115 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4219,712,629 - 19,801,443 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1219,634,740 - 19,688,742 (-)NCBI
Celera216,903,548 - 17,002,158 (-)NCBICelera
Cytogenetic Map2q12NCBI
VCAN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl583,471,618 - 83,582,303 (+)EnsemblGRCh38hg38GRCh38
GRCh38583,471,744 - 83,582,302 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37582,767,563 - 82,878,121 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36582,803,339 - 82,912,737 (+)NCBINCBI36hg18NCBI36
Build 34582,803,338 - 82,912,737NCBI
Celera578,672,557 - 78,783,162 (+)NCBI
Cytogenetic Map5q14.2-q14.3NCBI
HuRef577,975,785 - 78,086,373 (+)NCBIHuRef
CHM1_1582,200,193 - 82,311,247 (+)NCBICHM1_1
Vcan
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391389,803,429 - 89,891,146 (-)NCBIGRCm39mm39
GRCm39 Ensembl1389,803,431 - 89,890,628 (-)Ensembl
GRCm381389,655,309 - 89,743,027 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1389,655,312 - 89,742,509 (-)EnsemblGRCm38mm10GRCm38
MGSCv371389,794,915 - 89,882,117 (-)NCBIGRCm37mm9NCBIm37
MGSCv361390,129,514 - 90,216,773 (-)NCBImm8
Celera1393,253,094 - 93,340,280 (-)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1345.5NCBI
Vcan
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541826,967,595 - 27,078,430 (-)NCBIChiLan1.0ChiLan1.0
VCAN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1532,019,709 - 32,130,350 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl532,019,709 - 32,130,351 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0531,699,278 - 31,810,169 (-)NCBIMhudiblu_PPA_v0panPan3
VCAN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl324,119,181 - 24,239,192 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1324,127,293 - 24,238,859 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Vcan
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364692,585,142 - 2,688,029 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCAN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl291,358,399 - 91,811,208 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1291,682,177 - 91,811,674 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2293,783,322 - 93,895,492 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VCAN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1477,581,627 - 77,692,495 (+)NCBI
ChlSab1.1 Ensembl477,593,449 - 77,690,616 (+)Ensembl
Vcan
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247433,635,086 - 3,743,332 (+)NCBI

Position Markers
RH134008  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q12UniSTS
RH143691  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0218,490,436 - 18,490,554NCBIRnor6.0
Rnor_5.0218,364,224 - 18,364,342UniSTSRnor5.0
RGSC_v3.4219,712,963 - 19,713,081UniSTSRGSC3.4
Celera216,903,882 - 16,904,000UniSTS
Cytogenetic Map2q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135167060Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21423783059237830Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141179397Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2789360052893600Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2541733642777046Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2944467949615930Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)2944467968866454Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)23127638105149020Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2541733621657459Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2368630848686308Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21055527555555275Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1336
Count of miRNA genes:308
Interacting mature miRNAs:399
Transcripts:ENSRNOT00000045532, ENSRNOT00000063821, ENSRNOT00000067456
Prediction methods:Microtar, Miranda, 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 32 6 6 6 1 1 63 21 33 4 1
Low 3 11 37 22 19 22 7 9 11 14 5 7 7
Below cutoff 14 13 13 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045532   ⟹   ENSRNOP00000045935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl218,514,668 - 18,565,842 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000063821   ⟹   ENSRNOP00000062961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl218,490,102 - 18,565,842 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067456   ⟹   ENSRNOP00000058873
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl218,490,102 - 18,565,842 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088313   ⟹   ENSRNOP00000074854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl218,492,018 - 18,531,210 (-)Ensembl
RefSeq Acc Id: NM_001170558   ⟹   NP_001164029
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2220,761,718 - 20,860,539 (-)NCBI
Rnor_6.0218,490,102 - 18,587,242 (-)NCBI
Rnor_5.0218,363,890 - 18,463,115 (-)NCBI
Celera216,903,548 - 17,002,060 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001170559   ⟹   NP_001164030
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2220,761,718 - 20,860,539 (-)NCBI
Rnor_6.0218,490,102 - 18,587,242 (-)NCBI
Rnor_5.0218,363,890 - 18,463,115 (-)NCBI
Celera216,903,548 - 17,002,060 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001170560   ⟹   NP_001164031
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2220,761,718 - 20,860,539 (-)NCBI
Rnor_6.0218,490,102 - 18,587,242 (-)NCBI
Rnor_5.0218,363,890 - 18,463,115 (-)NCBI
Celera216,903,548 - 17,002,060 (-)NCBI
Sequence:
RefSeq Acc Id: NM_053663   ⟹   NP_446115
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2220,761,718 - 20,860,637 (-)NCBI
Rnor_6.0218,490,102 - 18,587,340 (-)NCBI
Rnor_5.0218,363,890 - 18,463,115 (-)NCBI
Celera216,903,548 - 17,002,158 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446115   ⟸   NM_053663
- Peptide Label: isoform 2 precursor
- Sequence:
RefSeq Acc Id: NP_001164030   ⟸   NM_001170559
- Peptide Label: isoform 4 precursor
- UniProtKB: Q9ERB4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001164031   ⟸   NM_001170560
- Peptide Label: isoform 3 precursor
- UniProtKB: Q9ERB4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001164029   ⟸   NM_001170558
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9ERB4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058873   ⟸   ENSRNOT00000067456
RefSeq Acc Id: ENSRNOP00000045935   ⟸   ENSRNOT00000045532
RefSeq Acc Id: ENSRNOP00000062961   ⟸   ENSRNOT00000063821
RefSeq Acc Id: ENSRNOP00000074854   ⟸   ENSRNOT00000088313
Protein Domains
C-type lectin   EGF-like   Ig-like V-type   Link   Sushi

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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
MR/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
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)
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
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)
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
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)
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
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)
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
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)
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
WKY/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
WKY/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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619940 AgrOrtholog
Ensembl Genes ENSRNOG00000029212 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045935 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000058873 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000062961 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074854 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045532 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000063821 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000067456 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088313 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSPG_CTLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
  Link_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114122 UniProtKB/Swiss-Prot
NCBI Gene 114122 ENTREZGENE
Pfam EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-set UniProtKB/Swiss-Prot
  Xlink UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vcan PhenoGen
PRINTS LINKMODULE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot
  LINK_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LINK_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUSHI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CCP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGv UniProtKB/Swiss-Prot
  LINK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
  SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K944_RAT UniProtKB/TrEMBL
  CSPG2_RAT UniProtKB/Swiss-Prot
  D3Z9N6_RAT UniProtKB/TrEMBL
  D3ZFC3_RAT UniProtKB/TrEMBL
  D4A8Y6_RAT UniProtKB/TrEMBL
  Q9ERB4 ENTREZGENE
UniProt Secondary O08592 UniProtKB/Swiss-Prot
  O88564 UniProtKB/Swiss-Prot
  Q9R1K4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-22 Vcan  versican  Cspg2  chondroitin sulfate proteoglycan 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cspg2  chondroitin sulfate proteoglycan 2    chondroitin sulfate proteoglycan 2 (versican)  Name updated 1299863 APPROVED
2002-08-07 Cspg2  chondroitin sulfate proteoglycan 2 (versican)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression present in vascular smooth muscle cells (SMCs) 632588
gene_expression localized around newly formed corpora lutea and vasculature immediately after ovulation 1299255
gene_regulation FSH and testosterone increase mRNA expression in ovarian tissue 1299255