Vcl (vinculin) - Rat Genome Database

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Gene: Vcl (vinculin) Rattus norvegicus
Analyze
Symbol: Vcl
Name: vinculin
RGD ID: 1311217
Description: Enables small GTPase binding activity. Predicted to be involved in several processes, including cell-cell junction assembly; platelet aggregation; and protein localization to cell surface. Predicted to act upstream of or within cell adhesion; plasma membrane bounded cell projection organization; and regulation of cell migration. Located in Z disc; intercalated disc; and sarcolemma. Colocalizes with actin filament; focal adhesion; and stress fiber. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1W; hypertrophic cardiomyopathy; and hypertrophic cardiomyopathy 15. Orthologous to human VCL (vinculin); PARTICIPATES IN E-cadherin signaling pathway; vascular endothelial growth factor signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,6-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC305679; metavinculin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
Celera151,235,777 - 1,325,408 (+)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1,8-cineole  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
aniline  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbamazepine  (ISO)
chloroprene  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
fenamidone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fructose  (EXP)
fumonisin B1  (ISO)
genistein  (ISO)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
griseofulvin  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroxychloroquine  (ISO)
imidacloprid  (EXP)
indometacin  (ISO)
ivermectin  (ISO)
leflunomide  (ISO)
methotrexate  (ISO)
microcystin RR  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
naphthalene  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
Nonylphenol  (ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
sodium sulfide (anhydrous)  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7816144   PMID:9415431   PMID:9700171   PMID:11732910   PMID:12203715   PMID:12473693   PMID:14657280   PMID:15128702   PMID:15883197   PMID:16481394   PMID:16803572   PMID:17893324  
PMID:18341635   PMID:19056867   PMID:19116150   PMID:19725078   PMID:20086044   PMID:20458337   PMID:21048959   PMID:21423176   PMID:22871113   PMID:22984613   PMID:23382103   PMID:24036928  
PMID:24623780   PMID:24769233   PMID:25204797   PMID:25217619   PMID:25424202   PMID:25468996   PMID:25753039   PMID:26316108   PMID:26359501   PMID:26437238   PMID:26923917   PMID:29162887  
PMID:30354218   PMID:30502091  


Genomics

Comparative Map Data
Vcl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
Celera151,235,777 - 1,325,408 (+)NCBICelera
Cytogenetic Map15p16NCBI
VCL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1073,995,193 - 74,121,363 (+)EnsemblGRCh38hg38GRCh38
GRCh381073,998,116 - 74,121,363 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371075,757,874 - 75,881,121 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361075,427,878 - 75,549,924 (+)NCBINCBI36hg18NCBI36
Build 341075,427,877 - 75,549,918NCBI
Celera1069,043,066 - 69,165,189 (+)NCBI
Cytogenetic Map10q22.2NCBI
HuRef1069,753,196 - 69,875,221 (+)NCBIHuRef
CHM1_11076,039,663 - 76,161,889 (+)NCBICHM1_1
Vcl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391420,979,436 - 21,083,744 (+)NCBIGRCm39mm39
GRCm39 Ensembl1420,979,466 - 21,083,744 (+)Ensembl
GRCm381420,929,383 - 21,033,676 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1420,929,398 - 21,033,676 (+)EnsemblGRCm38mm10GRCm38
MGSCv371421,748,655 - 21,852,895 (+)NCBIGRCm37mm9NCBIm37
MGSCv361419,717,985 - 19,822,225 (+)NCBImm8
Celera1417,309,615 - 17,412,913 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1411.53NCBI
Vcl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543717,813,007 - 17,920,253 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543717,812,998 - 17,920,253 (-)NCBIChiLan1.0ChiLan1.0
VCL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11073,191,384 - 73,311,301 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1073,191,375 - 73,311,296 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01070,521,259 - 70,641,917 (+)NCBIMhudiblu_PPA_v0panPan3
VCL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1424,404,279 - 24,518,977 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl424,404,319 - 24,518,633 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha424,541,842 - 24,656,546 (+)NCBI
ROS_Cfam_1.0424,685,066 - 24,802,488 (+)NCBI
UMICH_Zoey_3.1424,581,947 - 24,697,844 (+)NCBI
UNSW_CanFamBas_1.0424,782,214 - 24,897,783 (+)NCBI
UU_Cfam_GSD_1.0425,137,362 - 25,252,305 (+)NCBI
Vcl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721356,558,734 - 56,670,307 (-)NCBI
SpeTri2.0NW_0049365215,051,077 - 5,163,036 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1476,700,168 - 76,811,875 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11476,700,143 - 76,811,875 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21482,826,487 - 82,938,103 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap14q2.5-q2.9NCBI
VCL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1957,253,219 - 57,375,947 (-)NCBI
ChlSab1.1 Ensembl957,255,166 - 57,376,028 (-)Ensembl
Vero_WHO_p1.0NW_02366604817,825,838 - 17,950,842 (-)NCBI
Vcl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247547,484,759 - 7,590,108 (+)NCBI

Position Markers
D15Got5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera151,243,608 - 1,243,802UniSTS
RH 3.4 Map1557.2UniSTS
RH 3.4 Map1557.2RGD
RH 2.0 Map150.0RGD
Cytogenetic Map15p16UniSTS
VCL  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,270,164 - 3,270,365 (+)MAPPERmRatBN7.2
Rnor_6.0153,459,600 - 3,459,800NCBIRnor6.0
Rnor_5.0153,437,910 - 3,438,110UniSTSRnor5.0
RGSC_v3.4153,482,603 - 3,482,803UniSTSRGSC3.4
Celera151,320,819 - 1,321,019UniSTS
Cytogenetic Map15p16UniSTS
RH133946  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,266,340 - 3,266,546 (+)MAPPERmRatBN7.2
Rnor_6.0153,455,776 - 3,455,981NCBIRnor6.0
Rnor_5.0153,434,086 - 3,434,291UniSTSRnor5.0
RGSC_v3.4153,478,779 - 3,478,984UniSTSRGSC3.4
Celera151,324,638 - 1,324,843UniSTS
RH 3.4 Map1563.2UniSTS
Cytogenetic Map15p16UniSTS
RH137914  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,266,846 - 3,266,983 (+)MAPPERmRatBN7.2
Rnor_6.0153,456,282 - 3,456,418NCBIRnor6.0
Rnor_5.0153,434,592 - 3,434,728UniSTSRnor5.0
RGSC_v3.4153,479,285 - 3,479,421UniSTSRGSC3.4
Celera151,324,201 - 1,324,337UniSTS
RH 3.4 Map1555.2UniSTS
Cytogenetic Map15p16UniSTS
RH139160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,267,387 - 3,267,550 (+)MAPPERmRatBN7.2
Rnor_6.0153,456,823 - 3,456,985NCBIRnor6.0
Rnor_5.0153,435,133 - 3,435,295UniSTSRnor5.0
RGSC_v3.4153,479,826 - 3,479,988UniSTSRGSC3.4
Celera151,323,634 - 1,323,796UniSTS
RH 3.4 Map1563.9UniSTS
Cytogenetic Map15p16UniSTS
BARC0060  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,277,886 - 3,279,331 (+)MAPPERmRatBN7.2
Rnor_6.0153,467,322 - 3,468,766NCBIRnor6.0
Rnor_5.0153,445,632 - 3,447,076UniSTSRnor5.0
RGSC_v3.4153,491,109 - 3,492,553UniSTSRGSC3.4
Celera151,311,853 - 1,313,297UniSTS
Cytogenetic Map15p16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:288
Count of miRNA genes:178
Interacting mature miRNAs:225
Transcripts:ENSRNOT00000015179
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


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 3 43 55 39 19 39 8 11 74 35 41 11 8
Low 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015179   ⟹   ENSRNOP00000015179
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0 Ensembl153,455,211 - 3,544,685 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085126   ⟹   ENSRNOP00000074748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0 Ensembl153,456,993 - 3,544,702 (-)Ensembl
RefSeq Acc Id: NM_001107248   ⟹   NP_001100718
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2153,265,776 - 3,355,523 (-)NCBI
Rnor_6.0153,455,211 - 3,544,685 (-)NCBI
Rnor_5.0153,433,521 - 3,522,441 (-)NCBI
RGSC_v3.4153,478,214 - 3,576,911 (-)RGD
Celera151,235,777 - 1,325,408 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251639   ⟹   XP_006251701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2153,265,810 - 3,355,586 (-)NCBI
Rnor_6.0153,455,248 - 3,544,738 (-)NCBI
Rnor_5.0153,433,521 - 3,522,441 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093231   ⟹   XP_038949159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2153,265,810 - 3,355,586 (-)NCBI
RefSeq Acc Id: XM_039093232   ⟹   XP_038949160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2153,265,810 - 3,355,586 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100718   ⟸   NM_001107248
- UniProtKB: P85972 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251701   ⟸   XM_006251639
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000074748   ⟸   ENSRNOT00000085126
RefSeq Acc Id: ENSRNOP00000015179   ⟸   ENSRNOT00000015179
RefSeq Acc Id: XP_038949160   ⟸   XM_039093232
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949159   ⟸   XM_039093231
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13699554
Promoter ID:EPDNEW_R10077
Type:multiple initiation site
Name:Vcl_1
Description:vinculin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0153,544,693 - 3,544,753EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/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
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: 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)
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/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
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)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:1311217 AgrOrtholog
Ensembl Genes ENSRNOG00000010765 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015179 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074748 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015179 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085126 UniProtKB/TrEMBL
InterPro Alpha-catenin/vinculin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin/catenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:305679 UniProtKB/Swiss-Prot
NCBI Gene 305679 ENTREZGENE
PANTHER PTHR46180 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vinculin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vcl PhenoGen
PROSITE VINCULIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VINCULIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K8V2_RAT UniProtKB/TrEMBL
  P85972 ENTREZGENE
  R9PXU6_RAT UniProtKB/TrEMBL
  VINC_RAT UniProtKB/Swiss-Prot
UniProt Secondary A6KKR4 UniProtKB/Swiss-Prot


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