Hspg2 (heparan sulfate proteoglycan 2) - Rat Genome Database
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Gene: Hspg2 (heparan sulfate proteoglycan 2) Rattus norvegicus
Analyze
Symbol: Hspg2
Name: heparan sulfate proteoglycan 2
RGD ID: 621770
Description: Exhibits collagen V binding activity. Involved in several processes, including animal organ regeneration; embryo implantation; and positive regulation of endothelial cell proliferation. Localizes to collagen-containing extracellular matrix. Biomarker of hypertension. Human ortholog(s) of this gene implicated in Schwartz-Jampel syndrome 1; Silverman-Handmaker type dyssegmental dysplasia; and osteochondrodysplasia. Orthologous to human HSPG2 (heparan sulfate proteoglycan 2); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,2,2-tetramine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: basement membrane-specific heparan sulfate proteoglycan core protein; LOC313641; Per; perlecan; perlecan (heparan sulfate proteoglycan 2)
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
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
Rnor_6.05155,812,096 - 155,913,751 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05159,568,612 - 159,669,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera5148,073,391 - 148,174,691 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bollineni JS, etal., Curr Eye Res. 1997 Feb;16(2):127-30.
2. Gallai M, etal., Biochem Biophys Res Commun. 1996 Nov 21;228(3):690-4.
3. Garl PJ, etal., Circ Res 2004 Feb 6;94(2):175-83. Epub 2003 Dec 1.
4. Jones JC, etal., J Cell Sci. 2005 Jun 15;118(Pt 12):2557-66. Epub 2005 May 31.
5. Ko CW, etal., Mol Cell Biochem 1996 Sep 6;162(1):65-73.
6. LaFramboise WA, etal., Mol Diagn Ther. 2006;10(3):187-96.
7. Li YZ, etal., Sheng Li Xue Bao. 2007 Apr 25;59(2):221-6.
8. Lipke DW, etal., Hypertension. 1993 Nov;22(5):743-53.
9. Lundmark K, etal., J Cell Physiol. 2001 Jul;188(1):67-74.
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Nicole S, etal., Nat Genet. 2000 Dec;26(4):480-3.
12. OMIM Disease Annotation Pipeline
13. Palma V, etal., Biol Res. 2011;44(1):63-7. doi: 10.4067/S0716-97602011000100008. Epub 2011 May 11.
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. RGD comprehensive gene curation
17. Rothblum K, etal., J Biol Chem. 2004 Dec 3;279(49):51282-8. Epub 2004 Sep 20.
18. Slater M and Murphy CR, Matrix Biol. 1999 Apr;18(2):125-31.
19. Tran PK, etal., Atherosclerosis. 2007 Feb;190(2):264-70. Epub 2006 Apr 18.
20. Vogl-Willis CA and Edwards IJ, Biochim Biophys Acta. 2004 Apr 7;1672(1):36-45.
21. Winkler S, etal., J Neurosci Res 2002 Aug 15;69(4):477-87.
Additional References at PubMed
PMID:7670489   PMID:10352025   PMID:10545953   PMID:10579729   PMID:11787818   PMID:11802174   PMID:12588956   PMID:12604605   PMID:12615671   PMID:15381701   PMID:15895400   PMID:15928325  
PMID:16407285   PMID:16502470   PMID:17525255   PMID:18757743   PMID:19056867   PMID:19199708   PMID:20551380   PMID:21126803   PMID:21289173   PMID:21362503   PMID:21423176   PMID:21747167  
PMID:21850672   PMID:22206666   PMID:22952693   PMID:23217742   PMID:23235151   PMID:23376485   PMID:23533145   PMID:23658023   PMID:23979707   PMID:24006456   PMID:25781054   PMID:26246161  
PMID:27068509   PMID:27559042   PMID:31505169  


Genomics

Comparative Map Data
Hspg2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
Rnor_6.05155,812,096 - 155,913,751 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05159,568,612 - 159,669,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera5148,073,391 - 148,174,691 (+)NCBICelera
Cytogenetic Map5q36NCBI
HSPG2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl121,822,244 - 21,937,310 (-)EnsemblGRCh38hg38GRCh38
GRCh38121,822,244 - 21,937,310 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37122,148,737 - 22,263,803 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36122,021,324 - 22,136,337 (-)NCBINCBI36hg18NCBI36
Build 34121,894,545 - 22,009,053NCBI
Celera120,471,674 - 20,545,742 (-)NCBI
Cytogenetic Map1p36.12NCBI
HuRef120,392,206 - 20,466,222 (-)NCBIHuRef
CHM1_1122,261,173 - 22,335,234 (-)NCBICHM1_1
Hspg2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394137,196,062 - 137,297,941 (+)NCBIGRCm39mm39
GRCm39 Ensembl4137,196,080 - 137,297,941 (+)Ensembl
GRCm384137,468,751 - 137,570,630 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4137,468,769 - 137,570,630 (+)EnsemblGRCm38mm10GRCm38
MGSCv374137,024,718 - 137,126,545 (+)NCBIGRCm37mm9NCBIm37
MGSCv364137,024,724 - 137,126,545 (+)NCBImm8
Celera4135,720,332 - 135,778,896 (+)NCBICelera
Cytogenetic Map4D3NCBI
cM Map469.93NCBI
Hspg2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554522,057,326 - 2,120,280 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554522,056,428 - 2,141,937 (-)NCBIChiLan1.0ChiLan1.0
HSPG2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1121,979,504 - 22,053,395 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl121,979,504 - 22,053,400 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0121,014,951 - 21,129,937 (-)NCBIMhudiblu_PPA_v0panPan3
HSPG2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl277,301,858 - 77,367,724 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1277,263,534 - 77,366,558 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hspg2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364747,407,622 - 7,478,950 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HSPG2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl679,849,687 - 79,958,271 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1679,849,691 - 79,958,283 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2673,882,694 - 73,947,389 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HSPG2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120110,693,858 - 110,809,467 (+)NCBI
ChlSab1.1 Ensembl20110,693,854 - 110,809,466 (+)Ensembl
Hspg2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247646,639,152 - 6,736,161 (-)NCBI

Position Markers
D5Rat66  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05155,835,939 - 155,836,107NCBIRnor6.0
Rnor_5.05159,592,438 - 159,592,606UniSTSRnor5.0
RGSC_v3.45156,250,789 - 156,250,957UniSTSRGSC3.4
RGSC_v3.45156,250,788 - 156,250,957RGDRGSC3.4
RGSC_v3.15156,260,828 - 156,260,996RGD
Celera5148,097,234 - 148,097,402UniSTS
RH 3.4 Map51009.5RGD
RH 3.4 Map51009.5UniSTS
RH 2.0 Map5942.8RGD
SHRSP x BN Map586.3899RGD
Cytogenetic Map5q36UniSTS
BE099553  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05155,831,009 - 155,831,176NCBIRnor6.0
Rnor_5.05159,587,508 - 159,587,675UniSTSRnor5.0
RGSC_v3.45156,245,859 - 156,246,026UniSTSRGSC3.4
Celera5148,092,304 - 148,092,471UniSTS
RH 3.4 Map51008.4UniSTS
Cytogenetic Map5q36UniSTS
RH129941  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05155,913,181 - 155,913,367NCBIRnor6.0
Rnor_5.05159,669,441 - 159,669,627UniSTSRnor5.0
RGSC_v3.45156,328,593 - 156,328,779UniSTSRGSC3.4
Celera5148,174,121 - 148,174,307UniSTS
RH 3.4 Map51009.6UniSTS
Cytogenetic Map5q36UniSTS
AU047918  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05155,835,795 - 155,836,033NCBIRnor6.0
Rnor_5.05159,592,294 - 159,592,532UniSTSRnor5.0
RGSC_v3.45156,250,645 - 156,250,883UniSTSRGSC3.4
Celera5148,097,090 - 148,097,328UniSTS
Cytogenetic Map5q36UniSTS
BM385095  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05155,842,533 - 155,842,707NCBIRnor6.0
Rnor_5.05159,599,032 - 159,599,206UniSTSRnor5.0
RGSC_v3.45156,257,392 - 156,257,566UniSTSRGSC3.4
Celera5148,103,829 - 148,104,003UniSTS
RH 3.4 Map51009.1UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134502140157212422Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149832180164807402Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5150340838164298744Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:133
Count of miRNA genes:92
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000039341, ENSRNOT00000055950
Prediction methods: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


Sequence


Reference Sequences
RefSeq Acc Id: XM_017593851   ⟹   XP_017449340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05155,812,096 - 155,913,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593852   ⟹   XP_017449341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,438 - 149,778,594 (+)NCBI
Rnor_6.05155,812,096 - 155,913,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603125   ⟹   XP_017458614
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera5148,073,391 - 148,174,691 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603126   ⟹   XP_017458615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera5148,073,391 - 148,174,691 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039111300   ⟹   XP_038967228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
RefSeq Acc Id: XM_039111301   ⟹   XP_038967229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
RefSeq Acc Id: XM_039111302   ⟹   XP_038967230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
RefSeq Acc Id: XM_039111303   ⟹   XP_038967231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,437 - 149,778,594 (+)NCBI
RefSeq Acc Id: XM_039111304   ⟹   XP_038967232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,438 - 149,778,594 (+)NCBI
RefSeq Acc Id: XM_039111305   ⟹   XP_038967233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,677,438 - 149,778,594 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_017458614   ⟸   XM_017603125
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017458615   ⟸   XM_017603126
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017449340   ⟸   XM_017593851
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017449341   ⟸   XM_017593852
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_038967228   ⟸   XM_039111300
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967229   ⟸   XM_039111301
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038967231   ⟸   XM_039111303
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967230   ⟸   XM_039111302
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038967232   ⟸   XM_039111304
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038967233   ⟸   XM_039111305
- Peptide Label: isoform X6
Protein Domains
LAM_G_DOMAIN


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)
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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
F344/NRrrc (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
FHH/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)
FHH/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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621770 AgrOrtholog
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
NCBI Gene Hspg2 ENTREZGENE
PhenoGen Hspg2 PhenoGen
PROSITE LAM_G_DOMAIN UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt O08591_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-03 Hspg2  heparan sulfate proteoglycan 2  LOC313641  perlecan  Data Merged 737654 APPROVED
2006-02-09 LOC313641  perlecan      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 Hspg2  heparan sulfate proteoglycan 2    perlecan (heparan sulfate proteoglycan 2)  Name updated 1299863 APPROVED
2002-08-07 Hspg2  perlecan (heparan sulfate proteoglycan 2)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression is reduced by glomerular adenylate cyclase 633166