Col1a2 (collagen type I alpha 2 chain) - Rat Genome Database

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Gene: Col1a2 (collagen type I alpha 2 chain) Rattus norvegicus
Analyze
Symbol: Col1a2
Name: collagen type I alpha 2 chain
RGD ID: 621351
Description: Predicted to enable several functions, including identical protein binding activity; platelet-derived growth factor binding activity; and protease binding activity. Predicted to be an extracellular matrix structural constituent. Involved in cellular response to retinoic acid; cellular response to thyroid hormone stimulus; and response to norepinephrine. Predicted to be located in endoplasmic reticulum. Predicted to be part of collagen type I trimer. Predicted to be active in extracellular matrix and extracellular space. Biomarker of hypothyroidism; muscular atrophy; pulmonary fibrosis; and ureteral obstruction. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome (multiple); heart valve disease; intracranial aneurysm; osteogenesis imperfecta (multiple); and osteoporosis. Orthologous to human COL1A2 (collagen type I alpha 2 chain); PARTICIPATES IN endothelin signaling pathway; interleukin-4 signaling pathway; syndecan signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alpha-2 type I collagen; collagen alpha-2(I) chain; collagen, type I, alpha 2; NEWGENE_621351; procollagen, type I, alpha 2
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
mRatBN7.2432,563,938 - 32,598,868 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0431,534,225 - 31,569,152 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl431,534,225 - 31,569,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0429,442,828 - 29,478,616 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0431,405,253 - 31,440,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4429,393,645 - 29,428,572 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1429,431,383 - 29,467,014 (+)NCBI
Celera427,947,892 - 27,982,658 (+)NCBICelera
Cytogenetic Map4q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-camphor  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
2-nitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5'-S-methyl-5'-thioadenosine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
9-cis-retinoic acid  (EXP)
acetaldehyde  (ISO)
acrylamide  (ISO)
actinomycin D  (EXP)
adenine  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
aldosterone  (ISO)
all-trans-retinoic acid  (EXP,ISO)
aluminium oxide  (ISO)
AM-251  (ISO)
amlodipine  (EXP)
amphetamine  (EXP)
amphibole asbestos  (EXP,ISO)
andrographolide  (EXP,ISO)
apocynin  (EXP)
Archazolid B  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
Atractylodin  (ISO)
baicalein  (EXP)
baicalin  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP,ISO)
boric acid  (ISO)
boron nitride  (ISO)
bosentan  (ISO)
bromochloroacetic acid  (EXP)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
camphor  (ISO)
candesartan  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chlordecone  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
cytochalasin D  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibromoacetic acid  (EXP)
diethylstilbestrol  (EXP,ISO)
Diosbulbin B  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (EXP)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP,ISO)
Ethoxyacetic acid  (ISO)
ferulic acid  (ISO)
flavonoids  (EXP)
flusilazole  (ISO)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP)
gamma-Oryzanol (TN)  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexaconazole  (ISO)
hydroxyurea  (ISO)
icariside II  (EXP)
ivermectin  (ISO)
L-ascorbic acid  (EXP,ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
lipoxin A4  (ISO)
lithium chloride  (ISO)
LY294002  (ISO)
magnesium atom  (ISO)
malathion  (ISO)
malonaldehyde  (EXP)
maraviroc  (ISO)
mercury dibromide  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mifepristone  (EXP)
Muraglitazar  (EXP)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naphthalene  (ISO)
nefazodone  (EXP)
nickel subsulfide  (EXP)
nicotinamide  (ISO)
nimesulide  (EXP)
nitric oxide  (EXP)
nitroprusside  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
p-chloromercuribenzoic acid  (ISO)
p-tert-Amylphenol  (EXP)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
pentane-2,3-dione  (EXP)
perindopril  (EXP)
Phenelzine  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
S-adenosyl-L-homocysteine  (ISO)
S-adenosyl-L-methioninate  (EXP,ISO)
S-adenosyl-L-methionine  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
salvianolic acid B  (EXP)
SB 203580  (EXP)
SB 431542  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium dichromate  (EXP)
sulindac  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thalidomide  (EXP)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP,ISO)
tributylstannane  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP,ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
Y-27632  (ISO)
zinc atom  (ISO)
zinc(0)  (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. Anania FA, etal., Free Radic Biol Med. 2001 Apr 15;30(8):846-57.
2. Arosio B, etal., Pharmacol Toxicol. 1993 Dec;73(6):301-4.
3. Bhambi B and Eghbali M, Am J Pathol. 1991 Nov;139(5):1131-42.
4. Chipman SD, etal., Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1701-5.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Hirose T, etal., J Appl Physiol. 2008 Jan;104(1):170-7. Epub 2007 Oct 4.
8. Klein LE, etal., J Mol Cell Cardiol. 1996 Jan;28(1):33-42.
9. Lee KS, etal., Hum Mutat. 2006 Jun;27(6):599.
10. Ling XB, etal., J Am Soc Nephrol. 2010 Apr;21(4):646-53. doi: 10.1681/ASN.2009080876. Epub 2010 Feb 11.
11. Malfait F, etal., J Med Genet. 2006 Jul;43(7):e36.
12. MGD data from the GO Consortium
13. Mouse Genome Database (MGD)
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. Online Mendelian Inheritance in Man, OMIM (TM).
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. RGD comprehensive gene curation
23. Schwarze U, etal., Am J Hum Genet. 2004 May;74(5):917-30. Epub 2004 Apr 9.
24. Sengupta PK, etal., J Biol Chem 2002 Jul 12;277(28):24926-37.
25. Superti-Furga A, etal., J Med Genet 1989 Jun;26(6):358-62.
26. Tahashi Y, etal., Hepatology. 2002 Jan;35(1):49-61.
27. Terashima H, etal., Am J Physiol Renal Physiol. 2010 Oct;299(4):F792-801. Epub 2010 Jul 21.
28. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
29. Yang Z, etal., Genet Mol Res. 2011 Feb 8;10(1):177-85. doi: 10.4238/vol10-1gmr984.
30. Yao J and Eghbali M, Circ Res. 1992 Oct;71(4):831-9.
31. Yoneyama T, etal., Stroke. 2004 Feb;35(2):443-8. Epub 2004 Jan 22.
32. Zhang K, etal., Lab Invest. 1994 Feb;70(2):192-202.
Additional References at PubMed
PMID:1590760   PMID:4435743   PMID:4636752   PMID:4763308   PMID:5337886   PMID:5443712   PMID:5544653   PMID:5785232   PMID:6395893   PMID:7825727   PMID:8686743   PMID:8841196  
PMID:8900172   PMID:9213002   PMID:10608859   PMID:12477932   PMID:12704794   PMID:12968017   PMID:14559231   PMID:17211858   PMID:17217948   PMID:17334644   PMID:17662583   PMID:17955022  
PMID:18375391   PMID:19156436   PMID:19362560   PMID:19755419   PMID:19932771   PMID:20053668   PMID:20548288   PMID:20551380   PMID:21362503   PMID:22049076   PMID:22910579   PMID:23399546  
PMID:23658023   PMID:24006456   PMID:24782617   PMID:25655816   PMID:25931508   PMID:27068509   PMID:27559042   PMID:30053369  


Genomics

Comparative Map Data
Col1a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2432,563,938 - 32,598,868 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0431,534,225 - 31,569,152 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl431,534,225 - 31,569,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0429,442,828 - 29,478,616 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0431,405,253 - 31,440,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4429,393,645 - 29,428,572 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1429,431,383 - 29,467,014 (+)NCBI
Celera427,947,892 - 27,982,658 (+)NCBICelera
Cytogenetic Map4q21NCBI
COL1A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl794,394,895 - 94,431,227 (+)EnsemblGRCh38hg38GRCh38
GRCh38794,394,895 - 94,431,227 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37794,024,207 - 94,060,539 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36793,861,809 - 93,898,480 (+)NCBINCBI36hg18NCBI36
Build 34793,668,523 - 93,705,195NCBI
Celera788,722,142 - 88,758,790 (+)NCBI
Cytogenetic Map7q21.3NCBI
HuRef788,631,579 - 88,668,235 (+)NCBIHuRef
CHM1_1793,953,972 - 93,990,650 (+)NCBICHM1_1
CRA_TCAGchr7v2793,353,052 - 93,389,700 (+)NCBI
Col1a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3964,505,618 - 4,541,543 (+)NCBIGRCm39mm39
GRCm39 Ensembl64,504,814 - 4,541,544 (+)Ensembl
GRCm3864,505,618 - 4,541,543 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl64,504,814 - 4,541,544 (+)EnsemblGRCm38mm10GRCm38
MGSCv3764,455,697 - 4,491,543 (+)NCBIGRCm37mm9NCBIm37
MGSCv3664,455,761 - 4,490,730 (+)NCBImm8
Celera64,648,226 - 4,684,066 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.81NCBI
Col1a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543211,128,112 - 11,163,302 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543211,127,961 - 11,164,145 (+)NCBIChiLan1.0ChiLan1.0
COL1A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1799,935,185 - 99,971,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl799,935,185 - 99,971,803 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0786,344,657 - 86,381,282 (+)NCBIMhudiblu_PPA_v0panPan3
COL1A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11419,883,731 - 19,919,527 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1419,883,868 - 19,919,527 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1419,443,112 - 19,478,898 (+)NCBI
ROS_Cfam_1.01419,699,099 - 19,734,901 (+)NCBI
ROS_Cfam_1.0 Ensembl1419,699,098 - 19,734,902 (+)Ensembl
UMICH_Zoey_3.11419,850,793 - 19,886,662 (+)NCBI
UNSW_CanFamBas_1.01419,585,955 - 19,621,759 (+)NCBI
UU_Cfam_GSD_1.01419,843,097 - 19,878,889 (+)NCBI
Col1a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511833,176,893 - 33,212,967 (+)NCBI
SpeTri2.0NW_0049365855,650,322 - 5,686,393 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL1A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl974,173,931 - 74,210,398 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1974,174,484 - 74,210,407 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2981,357,192 - 81,393,118 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL1A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12154,602,780 - 54,639,832 (-)NCBIChlSab1.1chlSab2
ChlSab1.12154,602,780 - 54,639,832 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2154,602,398 - 54,632,780 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604249,682,896 - 49,719,954 (+)NCBIVero_WHO_p1.0
Col1a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248131,174,071 - 1,209,929 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat151  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,583,980 - 32,584,199 (+)MAPPERmRatBN7.2
Rnor_6.0431,554,266 - 31,554,484NCBIRnor6.0
Rnor_6.0429,549,895 - 29,550,113NCBIRnor6.0
Rnor_5.0429,463,219 - 29,463,437UniSTSRnor5.0
Rnor_5.0431,425,294 - 31,425,512UniSTSRnor5.0
RGSC_v3.4429,413,655 - 29,414,068RGDRGSC3.4
RGSC_v3.4429,413,686 - 29,413,904UniSTSRGSC3.4
RGSC_v3.1429,452,129 - 29,452,347RGD
Celera427,967,860 - 27,968,078UniSTS
RH 3.4 Map4449.82UniSTS
RH 3.4 Map4449.82RGD
RH 2.0 Map4215.3RGD
SHRSP x BN Map417.0799RGD
Cytogenetic Map4q13UniSTS
RH132451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,598,608 - 32,598,800 (+)MAPPERmRatBN7.2
Rnor_6.0429,564,522 - 29,564,713NCBIRnor6.0
Rnor_6.0431,568,893 - 31,569,084NCBIRnor6.0
Rnor_5.0431,439,921 - 31,440,112UniSTSRnor5.0
Rnor_5.0429,477,846 - 29,478,037UniSTSRnor5.0
RGSC_v3.4429,428,313 - 29,428,504UniSTSRGSC3.4
Celera427,982,399 - 27,982,590UniSTS
RH 3.4 Map4435.74UniSTS
Cytogenetic Map4q13UniSTS
RH133324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,599,105 - 32,599,295 (+)MAPPERmRatBN7.2
Rnor_6.0429,565,019 - 29,565,208NCBIRnor6.0
Rnor_6.0431,569,390 - 31,569,579NCBIRnor6.0
Rnor_5.0431,440,418 - 31,440,607UniSTSRnor5.0
Rnor_5.0429,478,343 - 29,478,532UniSTSRnor5.0
RGSC_v3.4429,428,810 - 29,428,999UniSTSRGSC3.4
Celera427,982,896 - 27,983,085UniSTS
RH 3.4 Map4435.74UniSTS
Cytogenetic Map4q13UniSTS
AI179432  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,584,697 - 32,584,884 (+)MAPPERmRatBN7.2
Rnor_6.0429,550,612 - 29,550,798NCBIRnor6.0
Rnor_6.0431,554,983 - 31,555,169NCBIRnor6.0
Rnor_5.0431,426,011 - 31,426,197UniSTSRnor5.0
Rnor_5.0429,463,936 - 29,464,122UniSTSRnor5.0
RGSC_v3.4429,414,403 - 29,414,589UniSTSRGSC3.4
Celera427,968,577 - 27,968,763UniSTS
Cytogenetic Map4q13UniSTS
AA819207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,597,337 - 32,598,521 (+)MAPPERmRatBN7.2
Rnor_6.0429,563,251 - 29,564,434NCBIRnor6.0
Rnor_6.0431,567,622 - 31,568,805NCBIRnor6.0
Rnor_5.0431,438,650 - 31,439,833UniSTSRnor5.0
Rnor_5.0429,476,575 - 29,477,758UniSTSRnor5.0
RGSC_v3.4429,427,042 - 29,428,225UniSTSRGSC3.4
Celera427,981,128 - 27,982,311UniSTS
RH 3.4 Map4219.24UniSTS
Cytogenetic Map4q13UniSTS
Col1a2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,597,213 - 32,598,399 (+)MAPPERmRatBN7.2
Rnor_6.0431,567,498 - 31,568,683NCBIRnor6.0
Rnor_6.0429,563,127 - 29,564,312NCBIRnor6.0
Rnor_5.0431,438,526 - 31,439,711UniSTSRnor5.0
Rnor_5.0429,476,451 - 29,477,636UniSTSRnor5.0
RGSC_v3.4429,426,918 - 29,428,103UniSTSRGSC3.4
Celera427,981,004 - 27,982,189UniSTS
Cytogenetic Map4q13UniSTS
GDB:177260  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.07139,647,866 - 139,648,445NCBIRnor5.0
Rnor_5.0429,475,523 - 29,476,477NCBIRnor5.0
Rnor_5.0431,437,598 - 31,438,552NCBIRnor5.0
RGSC_v3.4429,425,991 - 29,426,944UniSTSRGSC3.4
RGSC_v3.47136,680,091 - 136,680,669UniSTSRGSC3.4
Celera427,980,077 - 27,981,030UniSTS
Celera7125,590,621 - 125,591,199UniSTS
Cytogenetic Map4q13UniSTS
Cytogenetic Map7q36UniSTS
GDB:180350  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,589,485 - 32,590,378 (+)MAPPERmRatBN7.2
Rnor_6.0429,555,399 - 29,556,291NCBIRnor6.0
Rnor_6.0431,559,770 - 31,560,662NCBIRnor6.0
Rnor_5.0431,430,798 - 31,431,690UniSTSRnor5.0
Rnor_5.0429,468,723 - 29,469,615UniSTSRnor5.0
RGSC_v3.4429,419,190 - 29,420,082UniSTSRGSC3.4
Celera427,973,363 - 27,974,255UniSTS
Cytogenetic Map4q13UniSTS
Col1a2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,563,837 - 32,564,004 (+)MAPPERmRatBN7.2
Rnor_6.0431,534,125 - 31,534,291NCBIRnor6.0
Rnor_6.0429,529,754 - 29,529,920NCBIRnor6.0
Rnor_5.0431,405,153 - 31,405,319UniSTSRnor5.0
Rnor_5.0429,443,078 - 29,443,244UniSTSRnor5.0
RGSC_v3.4429,393,545 - 29,393,711UniSTSRGSC3.4
Celera427,947,792 - 27,947,958UniSTS
Cytogenetic Map4q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)42271068534430484Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:30
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000016423
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
Low 2 16 4 4 1 4 4 7 18 28 7 4
Below cutoff 1 23 29 23 8 23 2 2 47 9 9 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016423   ⟹   ENSRNOP00000016423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0 Ensembl431,534,225 - 31,569,151 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087619   ⟹   ENSRNOP00000073398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0 Ensembl429,535,852 - 29,564,768 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089292   ⟹   ENSRNOP00000075459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl431,534,225 - 31,568,806 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089564   ⟹   ENSRNOP00000069327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl429,529,854 - 29,564,435 (+)Ensembl
RefSeq Acc Id: NM_053356   ⟹   NP_445808
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2432,563,938 - 32,598,868 (+)NCBI
Rnor_6.0431,534,225 - 31,569,152 (+)NCBI
Rnor_5.0431,405,253 - 31,440,180 (+)NCBI
RGSC_v3.4429,393,645 - 29,428,572 (+)RGD
Celera427,947,892 - 27,982,658 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_445808   ⟸   NM_053356
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000075459   ⟸   ENSRNOT00000089292
RefSeq Acc Id: ENSRNOP00000016423   ⟸   ENSRNOT00000016423
RefSeq Acc Id: ENSRNOP00000073398   ⟸   ENSRNOT00000087619
RefSeq Acc Id: ENSRNOP00000069327   ⟸   ENSRNOT00000089564
Protein Domains
Fibrillar collagen NC1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
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
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)
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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
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)
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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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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)
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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)
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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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 (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