Col3a1 (collagen type III alpha 1 chain) - Rat Genome Database

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Gene: Col3a1 (collagen type III alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col3a1
Name: collagen type III alpha 1 chain
RGD ID: 71029
Description: Predicted to enable several functions, including integrin binding activity; platelet-derived growth factor binding activity; and protease binding activity. Predicted to be an extracellular matrix structural constituent. Involved in response to mechanical stimulus and skeletal system development. Located in collagen-containing extracellular matrix. Biomarker of bladder neck obstruction; glomerulosclerosis; myocardial infarction; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome; Ehlers-Danlos syndrome hypermobility type; end stage renal disease; and vascular type Ehlers-Danlos syndrome. Orthologous to human COL3A1 (collagen type III alpha 1 chain); PARTICIPATES IN endothelin signaling pathway; syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH (-)-epigallocatechin 3-gallate; (R)-noradrenaline; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: collagen alpha-1(III) chain; collagen, type III, alpha 1; MGC93704; procollagen type III alpha 1; procollagen, type III, alpha 1
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
mRatBN7.2947,374,611 - 47,410,547 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl947,374,593 - 47,410,547 (+)Ensembl
Rnor_6.0952,023,295 - 52,059,221 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,023,295 - 52,059,217 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0951,689,492 - 51,725,418 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,281,582 - 44,317,831 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1944,310,161 - 44,319,243 (+)NCBI
Celera945,061,755 - 45,097,754 (+)NCBICelera
RH 3.4 Map9388.09RGD
Cytogenetic Map9q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Otitis Media  (ISO)
alcoholic liver cirrhosis  (ISO)
Aneurysm  (ISO)
aortic aneurysm  (ISO)
aortic disease  (ISO)
aortic valve insufficiency  (ISO)
ARTERIAL DISSECTION  (ISO)
bladder neck obstruction  (IEP)
Chemical and Drug Induced Liver Injury  (ISO)
connective tissue disease  (ISO)
Contracture  (IEP)
Ehlers-Danlos syndrome  (ISO)
Ehlers-Danlos syndrome classic type 1  (ISO)
Ehlers-Danlos syndrome hypermobility type  (ISO)
Ehlers-Danlos Syndrome Type 4  (ISO)
end stage renal disease  (ISO)
endomyocardial fibrosis  (ISO)
epilepsy  (ISO)
Experimental Liver Cirrhosis  (ISO)
extrahepatic cholestasis  (ISO)
facioscapulohumeral muscular dystrophy  (ISO)
Familial Thoracic Aortic Aneurysm 1  (ISO)
Familial Thoracic Aortic Aneurysm 2  (ISO)
fatty liver disease  (ISO)
Fibrosis  (ISO)
genetic disease  (ISO)
glomerulosclerosis  (IEP)
Hernia, Ventral  (IDA)
Hypercholesterolemia  (ISO)
hyperglycemia  (ISO)
hyperinsulinism  (ISO)
hypertension  (ISO)
Keloid  (ISO)
Left Ventricular Hypertrophy  (ISO)
liver cirrhosis  (ISO)
liver disease  (ISO)
Loeys-Dietz syndrome  (ISO)
Marfan syndrome  (ISO)
Marfanoid Hypermobility Syndrome  (ISO)
Maxillofacial Abnormalities  (IDA)
megacolon  (ISO)
Mycoplasma pneumoniae pneumonia  (ISO)
myocardial infarction  (IEP)
nephrosclerosis  (ISO)
Neurodevelopmental Disorders  (ISO)
Polymicrogyria with or without Vascular-Type Ehlers-Danlos Syndrome  (ISO)
pulmonary fibrosis  (ISO)
renal fibrosis  (ISO)
schizophrenia  (ISO)
systemic scleroderma  (ISS)
thoracic aortic aneurysm  (ISO)
Transplant Rejection  (ISO)
type 2 diabetes mellitus  (IEP)
ureteral obstruction  (ISO)
vascular type Ehlers-Danlos syndrome  (ISO)
visual epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(-)-selegiline  (ISO)
(R)-noradrenaline  (EXP,ISO)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-butoxyethanol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-methylcholanthrene  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (EXP)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
Ac-Ser-Asp-Lys-Pro-OH  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
adenine  (EXP,ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (ISO)
aldosterone  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
ambroxol  (EXP)
ammonium chloride  (EXP)
amphibole asbestos  (EXP,ISO)
andrographolide  (EXP,ISO)
anthocyanin  (ISO)
apocynin  (EXP)
arsenic acid  (ISO)
arsenite(3-)  (ISO)
azelastine  (ISO)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bilirubin IXalpha  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP,ISO)
boron nitride  (ISO)
bucladesine  (ISO)
buspirone  (EXP)
C.I. Natural Red 20  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
camostat  (EXP)
Candesartan cilexetil  (EXP)
cannabidiol  (ISO)
capsaicin  (EXP)
captopril  (ISO)
carbon atom  (ISO)
carbon nanotube  (ISO)
carnosine  (ISO)
carvedilol  (EXP)
CGS-21680  (ISO)
chloroprene  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibric acid  (EXP)
clorgyline  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
DDT  (EXP)
Delta(9)-tetrahydrocannabinolic acid  (ISO)
dexamethasone  (EXP,ISO)
diclofenac  (EXP,ISO)
diethyl malate  (ISO)
diethyl maleate  (ISO)
Diosbulbin B  (ISO)
dioxygen  (EXP,ISO)
diprotium oxide  (EXP)
dipyridamole  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
diuron  (EXP)
divanadium pentaoxide  (ISO)
dizocilpine maleate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor  (EXP)
elemental carbon  (ISO)
emodin  (EXP)
enalapril  (EXP,ISO)
endosulfan  (EXP)
eplerenone  (EXP)
eprosartan  (EXP)
ergosta-4,6,8(14),22-tetraen-3-one  (ISO)
ethanol  (EXP)
excitatory amino acid agonist  (ISO)
fasudil  (ISO)
fenofibrate  (ISO)
fingolimod hydrochloride  (ISO)
folic acid  (ISO)
fulvestrant  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
griseofulvin  (ISO)
Honokiol  (ISO)
hydrogen peroxide  (ISO)
indometacin  (EXP)
isoprenaline  (EXP,ISO)
isotretinoin  (EXP)
ivermectin  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
limonene  (EXP)
linoleic acid  (ISO)
lipopolysaccharide  (EXP,ISO)
losartan  (EXP,ISO)
manidipine  (EXP)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methylglyoxal  (ISO)
methylmercury(1+)  (EXP)
methylparaben  (ISO)
methyltestosterone  (ISO)
metoprolol  (ISO)
mifepristone  (EXP)
Monobutylphthalate  (ISO)
monosodium L-glutamate  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
Nandrolone decanoate  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
Pachymic acid  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
paricalcitol  (ISO)
Pentoxifylline  (EXP)
perfluorooctanoic acid  (EXP)
perindopril  (EXP)
permethrin  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
Plantamajoside  (ISO)
poly(guanylic acid)  (EXP)
potassium dichromate  (ISO)
progesterone  (ISO)
puerarin  (EXP)
quercetin  (ISO)
quercitrin  (ISO)
Rebamipide  (EXP)
resveratrol  (EXP,ISO)
rosmarinic acid  (EXP)
rotenone  (EXP)
saralasin  (ISO)
sarin  (ISO)
SB 431542  (ISO)
SCH 23390  (EXP)
serpentine asbestos  (ISO)
Shikonin  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sorafenib  (ISO)
spironolactone  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetramethylpyrazine  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
topotecan  (EXP,ISO)
toxaphene  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
valsartan  (ISO)
vancomycin  (ISO)
verapamil  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (EXP)
water  (EXP)
Y-27632  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abrahamsen CT, etal., J Pharmacol Exp Ther. 2002 Apr;301(1):21-8. doi: 10.1124/jpet.301.1.21.
2. Abrass CK, etal., Am J Physiol Renal Physiol. 2011 Feb;300(2):F531-9. doi: 10.1152/ajprenal.00237.2010. Epub 2010 Jul 7.
3. Frankel FR, etal., DNA 1988 Jun;7(5):347-54.
4. Gaikwad AB, etal., Biochem J. 2010 Dec 1;432(2):333-41. doi: 10.1042/BJ20100414.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Glumoff V, etal., Biochim Biophys Acta 1994 Jan 18;1217(1):41-8.
7. GOA data from the GO Consortium
8. Imai C, etal., Clin Exp Hypertens 2005 Jan;27(1):59-69.
9. Kanazawa K, etal., Int J Clin Exp Pathol. 2015 Apr 1;8(4):3426-40. eCollection 2015.
10. Kim J, etal., J Microbiol Biotechnol. 2020 Mar 28;30(3):427-438. doi: 10.4014/jmb.1910.10055.
11. Kontusaari S, etal., Am J Hum Genet 1990 Jul;47(1):112-20.
12. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
13. Ling XB, etal., J Am Soc Nephrol. 2010 Apr;21(4):646-53. doi: 10.1681/ASN.2009080876. Epub 2010 Feb 11.
14. Marks SC Jr, etal., Dev Dyn 1999 Jun;215(2):117-25.
15. MGD Curation, June 12, 2002
16. Narcisi P, etal., Hum Mol Genet. 1994 Sep;3(9):1617-20.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Oderich GS, etal., J Vasc Surg. 2005 Jul;42(1):98-106.
19. OMIM Disease Annotation Pipeline
20. Online Mendelian Inheritance in Man, OMIM (TM).
21. Pepin M, etal., N Engl J Med 2000 Mar 9;342(10):673-80.
22. Phua YL, etal., J Pathol. 2013 Apr;229(5):685-96. doi: 10.1002/path.4155. Epub 2013 Feb 22.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. RGD comprehensive gene curation
28. Richards AJ, etal., Hum Genet. 1992 Jan;88(3):325-30.
29. Schroder A, etal., J Urol. 2013 Jun;189(6):2377-84. doi: 10.1016/j.juro.2012.12.110. Epub 2013 Jan 9.
30. Smith LB, etal., Cardiovasc Res. 2011 Apr 1;90(1):182-90. doi: 10.1093/cvr/cvq356. Epub 2010 Nov 10.
31. Sun HB, etal., J Orthop Res. 2010 Oct;28(10):1380-6. doi: 10.1002/jor.21132.
32. Van Eps J, etal., Surg Endosc. 2015 Nov 17.
33. Wong VY, etal., Br J Pharmacol. 2001 Nov;134(5):977-84. doi: 10.1038/sj.bjp.0704329.
34. Wurtz T, etal., Matrix Biol 1998 Oct;17(5):349-60.
35. Yang F, etal., J Cardiovasc Pharmacol. 2015 May;65(5):456-64. doi: 10.1097/FJC.0000000000000214.
36. Yoshida T, etal., Int J Mol Med. 2009 Jun;23(6):785-92.
Additional References at PubMed
PMID:1466622   PMID:2209468   PMID:7487954   PMID:7546986   PMID:7825727   PMID:8686743   PMID:8900172   PMID:8984825   PMID:9036918   PMID:9050868   PMID:9076960   PMID:9573018  
PMID:10022501   PMID:12477932   PMID:12810172   PMID:12810173   PMID:14559231   PMID:14575307   PMID:14736764   PMID:14970208   PMID:15489334   PMID:16360482   PMID:16754721   PMID:16912226  
PMID:17206378   PMID:17407709   PMID:17576241   PMID:17662583   PMID:18471258   PMID:18726071   PMID:19393425   PMID:19426591   PMID:19932771   PMID:20388018   PMID:20548288   PMID:21166192  
PMID:21729992   PMID:21768377   PMID:23658023   PMID:24006456   PMID:25784725   PMID:27068509   PMID:27363275   PMID:27559042   PMID:28320405   PMID:28436683   PMID:29286102   PMID:29476059  
PMID:32328952  


Genomics

Candidate Gene Status
Col3a1 is a candidate Gene for QTL Vetf6
Comparative Map Data
Col3a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2947,374,611 - 47,410,547 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl947,374,593 - 47,410,547 (+)Ensembl
Rnor_6.0952,023,295 - 52,059,221 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,023,295 - 52,059,217 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0951,689,492 - 51,725,418 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,281,582 - 44,317,831 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1944,310,161 - 44,319,243 (+)NCBI
Celera945,061,755 - 45,097,754 (+)NCBICelera
RH 3.4 Map9388.09RGD
Cytogenetic Map9q22NCBI
COL3A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2188,974,373 - 189,012,746 (+)EnsemblGRCh38hg38GRCh38
GRCh382188,974,373 - 189,012,746 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372189,839,099 - 189,877,472 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362189,547,344 - 189,585,717 (+)NCBINCBI36hg18NCBI36
Build 342189,664,604 - 189,702,978NCBI
Celera2183,433,958 - 183,472,272 (+)NCBI
Cytogenetic Map2q32.2NCBI
HuRef2181,698,732 - 181,737,119 (+)NCBIHuRef
CHM1_12189,845,032 - 189,883,377 (+)NCBICHM1_1
Col3a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,350,698 - 45,388,866 (+)NCBIGRCm39mm39
GRCm39 Ensembl145,350,698 - 45,388,866 (+)Ensembl
GRCm38145,311,538 - 45,349,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl145,311,538 - 45,349,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv37145,368,383 - 45,406,551 (+)NCBIGRCm37mm9NCBIm37
MGSCv36145,256,192 - 45,293,566 (+)NCBImm8
Celera145,612,466 - 45,650,861 (+)NCBICelera
Cytogenetic Map1C1.1NCBI
cM Map123.67NCBI
Col3a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554039,721,114 - 9,757,887 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554039,720,831 - 9,758,019 (-)NCBIChiLan1.0ChiLan1.0
COL3A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B194,204,613 - 194,242,956 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B194,204,613 - 194,242,956 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B76,285,115 - 76,322,703 (+)NCBIMhudiblu_PPA_v0panPan3
COL3A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13630,488,250 - 30,526,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3630,488,488 - 30,536,765 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3630,394,214 - 30,431,773 (+)NCBI
ROS_Cfam_1.03630,718,700 - 30,756,283 (+)NCBI
ROS_Cfam_1.0 Ensembl3630,718,908 - 30,756,954 (+)Ensembl
UMICH_Zoey_3.13630,779,325 - 30,816,837 (+)NCBI
UNSW_CanFamBas_1.03630,715,289 - 30,752,838 (+)NCBI
UU_Cfam_GSD_1.03630,884,313 - 30,921,873 (+)NCBI
Col3a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303147,914,117 - 147,951,851 (+)NCBI
SpeTri2.0NW_0049365068,886,494 - 8,923,921 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL3A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1593,556,912 - 93,615,815 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11593,556,914 - 93,595,678 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215104,067,018 - 104,105,776 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL3A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11074,455,133 - 74,493,392 (+)NCBIChlSab1.1chlSab2
ChlSab1.11074,455,133 - 74,493,392 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040124,979,692 - 125,017,963 (-)NCBIVero_WHO_p1.0
Col3a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248991,192,078 - 1,230,528 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134399  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,410,158 - 47,410,359 (+)MAPPERmRatBN7.2
Rnor_6.0952,058,833 - 52,059,033NCBIRnor6.0
Rnor_5.0951,725,030 - 51,725,230UniSTSRnor5.0
RGSC_v3.4944,317,443 - 44,317,643UniSTSRGSC3.4
Celera945,097,366 - 45,097,566UniSTS
Cytogenetic Map9q22UniSTS
X57983  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,410,341 - 47,410,514 (+)MAPPERmRatBN7.2
Rnor_6.0952,059,016 - 52,059,188NCBIRnor6.0
Rnor_5.0951,725,213 - 51,725,385UniSTSRnor5.0
RGSC_v3.4944,317,626 - 44,317,798UniSTSRGSC3.4
Celera945,097,549 - 45,097,721UniSTS
Cytogenetic Map9q22UniSTS
RH142444  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,410,305 - 47,410,464 (+)MAPPERmRatBN7.2
Rnor_6.0952,058,980 - 52,059,138NCBIRnor6.0
Rnor_5.0951,725,177 - 51,725,335UniSTSRnor5.0
RGSC_v3.4944,317,590 - 44,317,748UniSTSRGSC3.4
Celera945,097,513 - 45,097,671UniSTS
RH 3.4 Map9388.09UniSTS
Cytogenetic Map9q22UniSTS
GDB:181238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,409,198 - 47,410,233 (+)MAPPERmRatBN7.2
Rnor_6.0952,057,873 - 52,058,907NCBIRnor6.0
Rnor_5.0951,724,070 - 51,725,104UniSTSRnor5.0
RGSC_v3.4944,316,483 - 44,317,517UniSTSRGSC3.4
Celera945,096,406 - 45,097,440UniSTS
Cytogenetic Map9q22UniSTS
UniSTS:531307  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,384,011 - 47,384,727 (+)MAPPERmRatBN7.2
Rnor_6.0952,032,688 - 52,033,403NCBIRnor6.0
Rnor_5.0951,698,885 - 51,699,600UniSTSRnor5.0
Celera945,071,203 - 45,071,918UniSTS
Cytogenetic Map9q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92213332249968732Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:128
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000004956
Prediction methods:Microtar, 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 15 2 2 26 5 2
Medium 3 28 57 41 19 41 6 9 68 35 14 6 6
Low 6 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_032085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ005395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230038 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M21354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X70369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004956   ⟹   ENSRNOP00000004956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl947,374,593 - 47,410,547 (+)Ensembl
Rnor_6.0 Ensembl952,023,295 - 52,059,217 (+)Ensembl
RefSeq Acc Id: NM_032085   ⟹   NP_114474
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2947,374,611 - 47,410,547 (+)NCBI
Rnor_6.0952,023,295 - 52,059,221 (+)NCBI
Rnor_5.0951,689,492 - 51,725,418 (+)NCBI
RGSC_v3.4944,281,582 - 44,317,831 (+)RGD
Celera945,061,755 - 45,097,754 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_114474   ⟸   NM_032085
- Peptide Label: precursor
- UniProtKB: P13941 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004956   ⟸   ENSRNOT00000004956
Protein Domains
Fibrillar collagen NC1   VWFC

Transcriptome

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

Promoters
RGD ID:13696646
Promoter ID:EPDNEW_R7170
Type:initiation region
Name:Col3a1_1
Description:collagen type III alpha 1 chain
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_6.0952,023,281 - 52,023,341EPDNEW

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)
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 (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)
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
BXH3/CubMcwi (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
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)
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)
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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/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
FXLE18/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
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)
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
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)
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
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)
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
HXB31/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
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)
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
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)
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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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
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
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)
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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/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
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
LN/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
M520/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
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)
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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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
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)
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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
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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
WAG/RijCrl (2020)
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