Gpc5 (glypican 5) - Rat Genome Database
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Gene: Gpc5 (glypican 5) Rattus norvegicus
Analyze
Symbol: Gpc5
Name: glypican 5
RGD ID: 1308835
Description: Orthologous to human GPC5 (glypican 5); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH bisphenol A; indole-3-methanol; N-acetyl-L-cysteine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: glypican-5; LOC306157
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
mRatBN7.21592,207,275 - 93,644,054 (+)NCBI
Rnor_6.015100,283,131 - 101,776,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015105,221,065 - 105,224,752 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.015103,739,948 - 104,456,749 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41599,917,274 - 101,353,034 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11599,932,834 - 100,716,974 (+)NCBI
Celera1591,103,971 - 92,504,072 (+)NCBICelera
Cytogenetic Map15q23-q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:25931508  


Genomics

Comparative Map Data
Gpc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21592,207,275 - 93,644,054 (+)NCBI
Rnor_6.015100,283,131 - 101,776,838 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015105,221,065 - 105,224,752 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.015103,739,948 - 104,456,749 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41599,917,274 - 101,353,034 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11599,932,834 - 100,716,974 (+)NCBI
Celera1591,103,971 - 92,504,072 (+)NCBICelera
Cytogenetic Map15q23-q24NCBI
GPC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1391,398,621 - 92,873,682 (+)EnsemblGRCh38hg38GRCh38
GRCh381391,398,621 - 92,867,237 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371392,050,875 - 93,519,490 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361390,848,930 - 92,317,491 (+)NCBINCBI36hg18NCBI36
Build 341390,848,887 - 92,317,486NCBI
Celera1372,897,866 - 74,366,737 (+)NCBI
Cytogenetic Map13q31.3NCBI
HuRef1372,646,702 - 74,116,008 (+)NCBIHuRef
CHM1_11392,019,488 - 93,489,120 (+)NCBICHM1_1
Gpc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914115,329,640 - 116,762,604 (+)NCBIGRCm39mm39
GRCm39 Ensembl14115,329,647 - 116,762,591 (+)Ensembl
GRCm3814115,092,201 - 116,525,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14115,092,215 - 116,525,179 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714115,491,437 - 116,924,414 (+)NCBIGRCm37mm9NCBIm37
MGSCv3614113,974,089 - 115,406,638 (+)NCBImm8
Celera14113,683,044 - 115,103,380 (+)NCBICelera
Cytogenetic Map14E4NCBI
Gpc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540416,827,833 - 18,091,256 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540416,824,366 - 18,091,464 (-)NCBIChiLan1.0ChiLan1.0
GPC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11391,755,264 - 93,206,407 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1391,755,623 - 93,205,610 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01372,588,968 - 74,051,961 (+)NCBIMhudiblu_PPA_v0panPan3
GPC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12242,526,426 - 43,873,992 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2242,526,054 - 43,870,405 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2242,382,134 - 43,727,661 (+)NCBI
ROS_Cfam_1.02242,927,701 - 44,302,647 (+)NCBI
UMICH_Zoey_3.12242,610,360 - 43,958,749 (+)NCBI
UNSW_CanFamBas_1.02242,664,714 - 43,999,944 (+)NCBI
UU_Cfam_GSD_1.02242,665,638 - 44,009,293 (+)NCBI
Gpc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_024404945178,229,811 - 178,459,961 (+)NCBI
SpeTri2.0NW_00493647217,492,183 - 17,708,067 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1160,791,032 - 62,146,238 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11160,791,000 - 62,149,911 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21166,666,602 - 67,323,189 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GPC5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1370,294,405 - 71,729,729 (+)NCBI
Gpc5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624779982,178 - 1,712,772 (-)NCBI

Position Markers
D15Rat25  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,059,401 - 101,059,554NCBIRnor6.0
Rnor_5.015104,508,697 - 104,508,850UniSTSRnor5.0
RGSC_v3.415100,708,159 - 100,708,312UniSTSRGSC3.4
RGSC_v3.415100,708,158 - 100,708,312RGDRGSC3.4
RGSC_v3.115100,723,939 - 100,724,092RGD
Celera1591,866,627 - 91,866,780UniSTS
RH 3.4 Map15632.1UniSTS
RH 3.4 Map15632.1RGD
RH 2.0 Map15519.5RGD
SHRSP x BN Map1558.1398RGD
FHH x ACI Map1570.62RGD
Cytogenetic Map15q24UniSTS
D15Rat26  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015100,390,296 - 100,390,442NCBIRnor6.0
Rnor_5.015103,847,523 - 103,847,669UniSTSRnor5.0
RGSC_v3.415100,026,553 - 100,026,699UniSTSRGSC3.4
RGSC_v3.415100,026,552 - 100,026,699RGDRGSC3.4
RGSC_v3.115100,042,332 - 100,042,479RGD
Celera1591,210,749 - 91,210,895UniSTS
RH 3.4 Map15610.4RGD
RH 3.4 Map15610.4UniSTS
RH 2.0 Map15495.0RGD
SHRSP x BN Map1558.4498RGD
Cytogenetic Map15q24UniSTS
D15Rat103  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.415100,174,510 - 100,174,630UniSTSRGSC3.4
RGSC_v3.415100,174,509 - 100,174,630RGDRGSC3.4
RGSC_v3.115100,190,289 - 100,190,410RGD
Celera1591,343,541 - 91,343,661UniSTS
SHRSP x BN Map1558.5898RGD
SHRSP x BN Map1558.5898UniSTS
Cytogenetic Map15q24UniSTS
D15Rat155  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,088,037 - 101,088,275NCBIRnor6.0
Rnor_5.015104,537,328 - 104,537,566UniSTSRnor5.0
RGSC_v3.415100,736,071 - 100,736,310UniSTSRGSC3.4
RGSC_v3.415100,736,070 - 100,736,310RGDRGSC3.4
RGSC_v3.115100,751,851 - 100,752,090RGD
Celera1591,895,368 - 91,895,607UniSTS
RH 3.4 Map15629.4RGD
RH 3.4 Map15629.4UniSTS
RH 2.0 Map15513.5RGD
SHRSP x BN Map1558.1398RGD
Cytogenetic Map15q24UniSTS
D15Rat156  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,088,037 - 101,088,264NCBIRnor6.0
Rnor_5.015104,537,328 - 104,537,555UniSTSRnor5.0
RGSC_v3.415100,736,071 - 100,736,299UniSTSRGSC3.4
RGSC_v3.415100,736,070 - 100,736,299RGDRGSC3.4
RGSC_v3.115100,751,851 - 100,752,079RGD
Celera1591,895,368 - 91,895,596UniSTS
RH 3.4 Map15629.3RGD
RH 3.4 Map15629.3UniSTS
RH 2.0 Map15513.5RGD
SHRSP x BN Map1558.5898RGD
Cytogenetic Map15q24UniSTS
D15Got85  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015100,883,950 - 100,884,223NCBIRnor6.0
Rnor_5.015104,334,735 - 104,335,008UniSTSRnor5.0
RGSC_v3.415100,529,949 - 100,530,222UniSTSRGSC3.4
RGSC_v3.415100,529,949 - 100,530,222RGDRGSC3.4
RGSC_v3.115100,545,729 - 100,546,002RGD
Celera1591,695,859 - 91,696,114UniSTS
RH 3.4 Map15625.3UniSTS
RH 3.4 Map15625.3RGD
RH 2.0 Map15509.5RGD
Cytogenetic Map15q24UniSTS
RH131320  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,776,429 - 101,776,615NCBIRnor6.0
Rnor_5.015105,224,343 - 105,224,529UniSTSRnor5.0
RGSC_v3.415101,352,625 - 101,352,811UniSTSRGSC3.4
Celera1592,503,663 - 92,503,849UniSTS
RH 3.4 Map15634.3UniSTS
Cytogenetic Map15q24UniSTS
BF388001  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,331,881 - 101,332,060NCBIRnor6.0
Rnor_5.015104,779,095 - 104,779,274UniSTSRnor5.0
RGSC_v3.415100,949,126 - 100,949,305UniSTSRGSC3.4
Celera1592,105,031 - 92,105,210UniSTS
RH 3.4 Map15618.2UniSTS
Cytogenetic Map15q24UniSTS
BF402049  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,020,468 - 101,020,564NCBIRnor6.0
Celera1591,831,069 - 91,831,166UniSTS
RH 3.4 Map15629.5UniSTS
Cytogenetic Map15q24UniSTS
AU048228  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015100,840,300 - 100,840,588NCBIRnor6.0
Rnor_5.015104,291,085 - 104,291,373UniSTSRnor5.0
RGSC_v3.415100,486,451 - 100,486,739UniSTSRGSC3.4
Celera1591,652,335 - 91,652,621UniSTS
Cytogenetic Map15q24UniSTS
BF415743  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015100,285,207 - 100,285,321NCBIRnor6.0
Rnor_5.015103,742,024 - 103,742,138UniSTSRnor5.0
RGSC_v3.41599,919,352 - 99,919,466UniSTSRGSC3.4
Celera1591,106,051 - 91,106,165UniSTS
RH 3.4 Map15608.4UniSTS
Cytogenetic Map15q24UniSTS
D5S680  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015101,746,315 - 101,747,700NCBIRnor6.0
Rnor_6.015101,746,716 - 101,747,700NCBIRnor6.0
Rnor_5.015105,194,630 - 105,195,614UniSTSRnor5.0
Rnor_5.015105,194,229 - 105,195,614UniSTSRnor5.0
RGSC_v3.415101,322,911 - 101,323,895UniSTSRGSC3.4
Celera1592,473,850 - 92,474,931UniSTS
Cytogenetic Map15q24UniSTS
AFM350VD1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015100,586,361 - 100,586,798NCBIRnor6.0
Rnor_6.0149,276,013 - 9,276,645NCBIRnor6.0
Rnor_5.015104,043,439 - 104,043,876UniSTSRnor5.0
Rnor_5.0149,237,569 - 9,238,201UniSTSRnor5.0
RGSC_v3.415100,232,059 - 100,232,496UniSTSRGSC3.4
RGSC_v3.4148,954,774 - 8,955,406UniSTSRGSC3.4
Celera1591,402,387 - 91,402,824UniSTS
Celera147,822,897 - 7,823,529UniSTS
Cytogenetic Map15q24UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)1561447766106447766Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1562596410103164962Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1565520564110520564Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1575527634111246239Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1575761024109400896Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1581255292103165069Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1581255292109133904Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)1581255430103164962Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1583947714111246239Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1584050550111246239Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1584050550111246239Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1589640684106550657Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)1589640684106550657Rat
1581519Cm59Cardiac mass QTL 592.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1596777066104003672Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:85
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000057664
Prediction methods:Microtar, 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: NM_001107285   ⟹   NP_001100755
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,239,546 - 93,644,054 (+)NCBI
Rnor_6.015100,283,131 - 101,776,838 (+)NCBI
Rnor_5.015103,739,948 - 104,456,749 (+)NCBI
Rnor_5.015105,221,065 - 105,224,752 (+)NCBI
RGSC_v3.41599,917,274 - 101,353,034 (+)RGD
Celera1591,103,971 - 92,504,072 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093411   ⟹   XP_038949339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,238,785 - 93,643,255 (+)NCBI
RefSeq Acc Id: XM_039093412   ⟹   XP_038949340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,238,781 - 92,610,057 (+)NCBI
RefSeq Acc Id: XM_039093413   ⟹   XP_038949341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,207,277 - 93,644,054 (+)NCBI
RefSeq Acc Id: XM_039093414   ⟹   XP_038949342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,207,275 - 93,644,054 (+)NCBI
RefSeq Acc Id: XR_005493739
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21592,238,785 - 93,643,232 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100755   ⟸   NM_001107285
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_038949342   ⟸   XM_039093414
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949341   ⟸   XM_039093413
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949340   ⟸   XM_039093412
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949339   ⟸   XM_039093411
- Peptide Label: isoform X1


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)
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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)
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)
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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:1308835 AgrOrtholog
NCBI Gene 306157 ENTREZGENE
PhenoGen Gpc5 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Gpc5  glypican 5   Gpc5_predicted  glypican 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gpc5_predicted  glypican 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED