Cd44 (CD44 molecule (Indian blood group)) - Rat Genome Database

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Gene: Cd44 (CD44 molecule (Indian blood group)) Rattus norvegicus
Analyze
Symbol: Cd44
Name: CD44 molecule (Indian blood group)
RGD ID: 2307
Description: Enables epidermal growth factor receptor binding activity; phosphoprotein binding activity; and protein kinase binding activity. Involved in several processes, including blood vessel maturation; macrophage fusion; and positive regulation of neutrophil apoptotic process. Located in apical plasma membrane; basolateral plasma membrane; and nucleus. Part of protein-containing complex. Biomarker of borna disease and cholestasis. Human ortholog(s) of this gene implicated in breast carcinoma (multiple); carcinoma (multiple); and prostate cancer. Orthologous to human CD44 (CD44 molecule (Indian blood group)); PARTICIPATES IN cell-extracellular matrix signaling pathway; INTERACTS WITH (+)-schisandrin B; (S)-colchicine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CD44 antigen; CD44 antigen isoform d6-12; CD44 antigen isoform d6-13; CD44 antigen isoform d6-15; Cd44 molecule; CD44A; cell surface glycoprotein CD44 (hyaluronate binding protein); ECMR-III; extracellular matrix receptor III; GP90 lymphocyte homing/adhesion receptor; hermes antigen; HUTCH-I; hyaluronate receptor; METAA; MGC124941; PGP-1; PGP-I; phagocytic glycoprotein 1; phagocytic glycoprotein I; RHAMM
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
mRatBN7.2389,155,850 - 89,244,615 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl389,157,058 - 89,244,620 (-)Ensembl
Rnor_6.0392,695,083 - 92,783,820 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl392,696,313 - 92,783,658 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0399,338,248 - 99,426,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4388,022,962 - 88,110,352 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1387,919,389 - 88,006,780 (-)NCBI
Celera388,236,830 - 88,324,125 (-)NCBICelera
RH 3.4 Map3656.5RGD
RH 3.4 Map3669.0RGD
Cytogenetic Map3q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (ISO)
(+)-schisandrin B  (EXP)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-mevalonic acid  (ISO)
(S)-colchicine  (EXP)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-acetamidofluorene  (EXP,IEP)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (EXP,ISO)
acrolein  (ISO)
acrylamide  (EXP,ISO)
Actein  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
albuterol  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
auramine O  (ISO)
Azaspiracid  (ISO)
bacitracin  (EXP)
bathocuproine disulfonic acid  (ISO)
beclomethasone  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzoates  (ISO)
beryllium sulfate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
Butylparaben  (EXP)
butyric acid  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP)
carmustine  (ISO)
casticin  (ISO)
chlorogenic acid  (ISO)
chlorpromazine  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
ciprofloxacin  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumestrol  (ISO)
crizotinib  (ISO)
crocidolite asbestos  (EXP,ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cytarabine  (ISO)
D-glucose  (ISO)
DDE  (EXP)
decabromodiphenyl ether  (EXP)
deguelin  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinous acid  (ISO)
dinophysistoxin 1  (ISO)
dioxygen  (ISO)
diuron  (EXP)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzacamene  (EXP)
enzyme inhibitor  (ISO)
epoxiconazole  (EXP)
ethanol  (EXP)
etodolac  (ISO)
etoposide  (ISO)
eugenol  (ISO)
fipronil  (EXP)
fisetin  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
formoterol fumarate  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
Gimeracil  (EXP)
glucose  (ISO)
glycidol  (EXP)
glycine betaine  (EXP)
glyphosate  (ISO)
graphite  (EXP)
hexestrol  (ISO)
Honokiol  (ISO)
hyaluronic acid  (ISO)
hydrogen peroxide  (ISO)
indometacin  (EXP)
ionomycin  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
iron(III) nitrilotriacetate  (EXP)
ivermectin  (ISO)
kaempferol  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
lapatinib  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
lithium chloride  (ISO)
lovastatin  (ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP)
melamine  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
mestranol  (ISO)
methapyrilene  (ISO)
methoxychlor  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
O-methyleugenol  (ISO)
ochratoxin A  (EXP)
okadaic acid  (ISO)
Osajin  (ISO)
ozone  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
Pomiferin  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (EXP,ISO)
propiconazole  (ISO)
pyrrolidine dithiocarbamate  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
reactive oxygen species  (ISO)
reparixin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
Salinomycin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
stattic  (ISO)
succimer  (ISO)
T-2 toxin  (ISO)
tacrolimus hydrate  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
theaflavin  (ISO)
thioacetamide  (EXP)
thymoquinone  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
trifluoperazine  (ISO)
trimethyltin  (ISO)
triphenylstannane  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (EXP)
verapamil  (ISO)
vincaleukoblastine  (EXP)
vinclozolin  (EXP)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blood vessel maturation  (IEP)
branching involved in prostate gland morphogenesis  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
cartilage development  (IEA,ISO)
cell adhesion  (IBA,IEA,IMP,ISO,NAS)
cell migration  (IMP,ISO)
cellular response to fibroblast growth factor stimulus  (IEA,ISO)
cytokine-mediated signaling pathway  (IEA)
hyaluronan catabolic process  (IEA,ISO)
inflammatory response  (IBA,IEP)
macrophage fusion  (IMP)
monocyte aggregation  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of CD4-positive, alpha-beta T cell proliferation  (ISO)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
negative regulation of DNA damage response, signal transduction by p53 class mediator  (IEA,ISO)
negative regulation of inflammatory response  (ISO)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (IEA,ISO)
negative regulation of mature B cell apoptotic process  (ISO)
negative regulation of regulatory T cell differentiation  (ISO)
neuron projection development  (IMP)
positive regulation of ERK1 and ERK2 cascade  (IBA,IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of heterotypic cell-cell adhesion  (IEA,ISO)
positive regulation of kinase activity  (ISO)
positive regulation of monocyte aggregation  (IEA,ISO)
positive regulation of neutrophil apoptotic process  (IMP)
positive regulation of peptidyl-serine phosphorylation  (IEA,ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
regulation of cell growth  (IDA)
regulation of lamellipodium morphogenesis  (IEA,ISO,ISS)
response to nutrient levels  (IEP)
response to organic cyclic compound  (IEP)
response to vitamin A  (IEP)
T cell activation  (IEA,ISO)
Wnt signaling pathway  (ISO)
wound healing involved in inflammatory response  (ISO)
wound healing, spreading of cells  (IEA,ISO,ISS)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Adriani W, etal., Ann N Y Acad Sci. 2006 Aug;1074:52-73.
2. Afify A, etal., Appl Immunohistochem Mol Morphol. 2007 Dec;15(4):446-50.
3. Afify AM, etal., Ann Diagn Pathol. 2005 Dec;9(6):312-8.
4. Al Qteishat A, etal., Neuroreport. 2006 Jul 31;17(11):1111-4.
5. Al-Amodi HSAB, etal., Cancer Invest. 2018 Mar 16;36(3):185-189. doi: 10.1080/07357907.2018.1445262. Epub 2018 Mar 14.
6. Arch R, etal., Science 1992 Jul 31;257(5070):682-5.
7. Arnaud JP, etal., Minerva Chir 1990 Feb;45(3-4):137-40.
8. Berner HS and Nesland JM, Breast Cancer Res Treat. 2001 Jan;65(1):23-9.
9. Carmo AM, etal., Eur J Immunol. 1993 Sep;23(9):2196-201.
10. Chen MJ, etal., Acta Obstet Gynecol Scand. 2005 Apr;84(4):322-8.
11. Cui W, etal., Blood. 2006 Jan 15;107(2):796-805. Epub 2005 Sep 29.
12. Decleves AE, etal., Int J Mol Med. 2006 Jul;18(1):83-94.
13. Fang M, etal., World J Gastrointest Oncol. 2020 Jan 15;12(1):66-76. doi: 10.4251/wjgo.v12.i1.66.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. Ghanem MA, etal., J Urol. 2002 Aug;168(2):681-6.
16. Gunthert U, etal., Cell 1991 Apr 5;65(1):13-24.
17. Halloran MM, etal., Arthritis Rheum. 1996 May;39(5):810-9.
18. Hellman U, etal., Cell Tissue Res. 2008 Jan 15;.
19. Hellstrom M, etal., Cells Tissues Organs. 2005;179(3):102-8.
20. Katoh S, etal., J Clin Invest. 2003 May;111(10):1563-70.
21. Khan SR, etal., Kidney Int. 2006 Sep;70(5):914-23. Epub 2006 Jul 19.
22. Kim Y, etal., Mol Immunol. 2011 Apr;48(8):1035-45. Epub 2011 Feb 23.
23. Kuo KT, etal., Mod Pathol. 2006 Dec;19(12):1570-7. Epub 2006 Sep 22.
24. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
25. Lian ZQ, etal., Ai Zheng. 2006 Oct;25(10):1291-5.
26. Lim SD, etal., Virchows Arch. 2008 Jan;452(1):49-55. Epub 2007 Nov 20.
27. Liu YJ, etal., World J Gastroenterol. 2005 Nov 14;11(42):6601-6.
28. Lou G, etal., World J Gastroenterol. 2005 Aug 28;11(32):5032-6.
29. Masuda M, etal., J Urol. 1999 Mar;161(3):805-8; discussion 808-9.
30. MGD data from the GO Consortium
31. Moon C, etal., J Vet Med Sci. 2006 Jul;68(7):761-4.
32. Morrison H, etal., Genes Dev. 2001 Apr 15;15(8):968-80.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Ouhtit A, etal., Am J Pathol. 2007 Dec;171(6):2033-9. Epub 2007 Nov 8.
35. Pipeline to import KEGG annotations from KEGG into RGD
36. Rangwala R, etal., J Biol Chem. 2005 Mar 25;280(12):11790-7. Epub 2005 Jan 19.
37. RGD automated data pipeline
38. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
39. RGD automated import pipeline for gene-chemical interactions
40. Ries A, etal., J Neurochem. 2007 Nov;103(4):1491-505. Epub 2007 Aug 30.
41. Sen M, etal., Eur Surg Res. 2006;38(3):347-52. Epub 2006 Jun 23.
42. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
43. Sun Y, etal., Zhonghua Yi Xue Za Zhi. 2005 Sep 14;85(35):2507-12.
44. Suzuki K, etal., J Bone Miner Res 2002 Aug;17(8):1486-97.
45. Takazoe K, etal., Kidney Int. 2000 Nov;58(5):1920-30.
46. Tawfik OW, etal., Arch Pathol Lab Med. 2007 Feb;131(2):261-7.
47. Williams BL, etal., Brain Pathol. 2006 Jan;16(1):1-14.
48. Woodson K, etal., Epigenetics. 2006 Oct-Dec;1(4):183-6.
49. Wu ST, etal., J Formos Med Assoc. 2003 Apr;102(4):229-33.
50. Yaqin M, etal., Scand J Infect Dis. 2007;39(5):441-8.
51. Zagorianakou N, etal., Eur J Gynaecol Oncol. 2003;24(6):500-4.
52. Zhu H, etal., Stem Cells. 2006 Apr;24(4):928-35. Epub 2005 Nov 23.
Additional References at PubMed
PMID:1469058   PMID:7528188   PMID:7538697   PMID:7584142   PMID:8043862   PMID:8769481   PMID:9133426   PMID:9324354   PMID:9374396   PMID:9472040   PMID:9692903   PMID:9847236  
PMID:10027409   PMID:10072077   PMID:10704459   PMID:10848813   PMID:10926769   PMID:10943842   PMID:11084024   PMID:11935029   PMID:11944887   PMID:12061795   PMID:12579564   PMID:12839939  
PMID:14609575   PMID:14764662   PMID:15100360   PMID:15212938   PMID:15294943   PMID:15477346   PMID:15531362   PMID:15624701   PMID:15691832   PMID:15701601   PMID:15728238   PMID:15843532  
PMID:16177108   PMID:16203996   PMID:16301745   PMID:16580085   PMID:16809613   PMID:16973387   PMID:17045821   PMID:17065554   PMID:17082577   PMID:17170110   PMID:17324121   PMID:17716972  
PMID:18056708   PMID:18085615   PMID:18450824   PMID:18556418   PMID:18638458   PMID:18694596   PMID:18958875   PMID:19008373   PMID:19047049   PMID:19056892   PMID:19199708   PMID:19208744  
PMID:19222954   PMID:19299737   PMID:19385056   PMID:19439532   PMID:19577615   PMID:19703720   PMID:19723499   PMID:19783662   PMID:19794968   PMID:19934022   PMID:20056122   PMID:20458337  
PMID:20470282   PMID:20522558   PMID:20711497   PMID:20962267   PMID:21423176   PMID:21460847   PMID:21508411   PMID:21708977   PMID:22072979   PMID:22470101   PMID:22692550   PMID:22726066  
PMID:23241663   PMID:23280959   PMID:23533145   PMID:23884413   PMID:25065622   PMID:25253654   PMID:25300795   PMID:25733665   PMID:26597578   PMID:26996509   PMID:27085217   PMID:27163367  
PMID:28871329   PMID:29175954   PMID:29589805   PMID:30951363   PMID:32223952   PMID:33450132  


Genomics

Comparative Map Data
Cd44
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2389,155,850 - 89,244,615 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl389,157,058 - 89,244,620 (-)Ensembl
Rnor_6.0392,695,083 - 92,783,820 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl392,696,313 - 92,783,658 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0399,338,248 - 99,426,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4388,022,962 - 88,110,352 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1387,919,389 - 88,006,780 (-)NCBI
Celera388,236,830 - 88,324,125 (-)NCBICelera
RH 3.4 Map3656.5RGD
RH 3.4 Map3669.0RGD
Cytogenetic Map3q32NCBI
CD44
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1135,138,882 - 35,232,402 (+)EnsemblGRCh38hg38GRCh38
GRCh381135,139,168 - 35,232,402 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371135,160,718 - 35,253,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361135,116,993 - 35,210,525 (+)NCBINCBI36hg18NCBI36
Build 341135,116,992 - 35,210,524NCBI
Celera1135,307,730 - 35,401,272 (+)NCBI
Cytogenetic Map11p13NCBI
HuRef1134,858,894 - 34,952,423 (+)NCBIHuRef
CHM1_11135,158,655 - 35,252,358 (+)NCBICHM1_1
Cd44
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392102,641,486 - 102,732,014 (-)NCBIGRCm39mm39
GRCm39 Ensembl2102,641,486 - 102,732,010 (-)Ensembl
GRCm382102,811,141 - 102,901,669 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2102,811,141 - 102,901,665 (-)EnsemblGRCm38mm10GRCm38
MGSCv372102,651,298 - 102,741,822 (-)NCBIGRCm37mm9NCBIm37
MGSCv362102,611,980 - 102,702,504 (-)NCBImm8
Celera2104,054,974 - 104,145,651 (-)NCBICelera
Cytogenetic Map2E2NCBI
cM Map254.13NCBI
Cd44
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542211,106,061 - 11,189,951 (-)NCBIChiLan1.0ChiLan1.0
CD44
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11134,985,634 - 35,132,900 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1134,985,634 - 35,079,009 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01135,110,732 - 35,258,238 (+)NCBIMhudiblu_PPA_v0panPan3
CD44
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11832,735,493 - 32,826,483 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1832,737,907 - 32,827,107 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1832,344,254 - 32,432,780 (-)NCBI
ROS_Cfam_1.01833,345,940 - 33,436,801 (-)NCBI
UMICH_Zoey_3.11832,909,118 - 32,997,479 (-)NCBI
UNSW_CanFamBas_1.01832,494,751 - 32,582,918 (-)NCBI
UU_Cfam_GSD_1.01833,135,283 - 33,223,633 (-)NCBI
Cd44
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494729,824,204 - 29,908,520 (-)NCBI
SpeTri2.0NW_0049365332,949,026 - 3,033,166 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD44
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl225,788,704 - 25,884,153 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1225,788,699 - 25,884,209 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2228,156,390 - 28,249,949 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD44
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1130,039,854 - 30,132,646 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl130,039,749 - 30,132,416 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038127,154,654 - 127,246,994 (-)NCBIVero_WHO_p1.0
Cd44
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476711,938,452 - 12,024,970 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC111028P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2389,158,688 - 89,158,782 (+)MAPPERmRatBN7.2
Rnor_6.0392,697,922 - 92,698,015NCBIRnor6.0
Rnor_5.0399,341,087 - 99,341,180UniSTSRnor5.0
RGSC_v3.4388,024,592 - 88,024,685UniSTSRGSC3.4
Celera388,238,460 - 88,238,553UniSTS
Cytogenetic Map3q31UniSTS
RH142186  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2389,157,588 - 89,157,763 (+)MAPPERmRatBN7.2
Rnor_6.0392,696,822 - 92,696,996NCBIRnor6.0
Rnor_5.0399,339,987 - 99,340,161UniSTSRnor5.0
RGSC_v3.4388,023,492 - 88,023,666UniSTSRGSC3.4
Celera388,237,360 - 88,237,534UniSTS
RH 3.4 Map3669.0UniSTS
Cytogenetic Map3q31UniSTS
RH94478  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2389,157,121 - 89,157,221 (+)MAPPERmRatBN7.2
Rnor_6.0392,696,355 - 92,696,454NCBIRnor6.0
Rnor_5.0399,339,520 - 99,339,619UniSTSRnor5.0
RGSC_v3.4388,023,025 - 88,023,124UniSTSRGSC3.4
Celera388,236,893 - 88,236,992UniSTS
Cytogenetic Map3q31UniSTS
RH134771  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2389,157,192 - 89,157,405 (+)MAPPERmRatBN7.2
Rnor_6.0392,696,426 - 92,696,638NCBIRnor6.0
Rnor_5.0399,339,591 - 99,339,803UniSTSRnor5.0
RGSC_v3.4388,023,096 - 88,023,308UniSTSRGSC3.4
Celera388,236,964 - 88,237,176UniSTS
RH 3.4 Map3669.0UniSTS
Cytogenetic Map3q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1272
Count of miRNA genes:245
Interacting mature miRNAs:300
Transcripts:ENSRNOT00000008760, ENSRNOT00000009000, ENSRNOT00000009073
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 21 20 10 19 10 4 4 2 17 11 4
Low 22 37 31 31 4 7 74 33 19 4
Below cutoff 5

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC109112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF014365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF065147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF295360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF295361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF295362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF295363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC107949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC127485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU366999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP901010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP901011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP901012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP901013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M61874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M61875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S41274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U46957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U52179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U96138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000008760   ⟹   ENSRNOP00000008760
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
Rnor_6.0 Ensembl392,697,833 - 92,749,121 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000009000   ⟹   ENSRNOP00000009000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
Rnor_6.0 Ensembl392,696,313 - 92,783,658 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000009073   ⟹   ENSRNOP00000009073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
Rnor_6.0 Ensembl392,697,571 - 92,783,569 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102139   ⟹   ENSRNOP00000097897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,210,186 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107007   ⟹   ENSRNOP00000096654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,058 - 89,244,620 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109066   ⟹   ENSRNOP00000078366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111131   ⟹   ENSRNOP00000090715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111172   ⟹   ENSRNOP00000080825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114481   ⟹   ENSRNOP00000090045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116432   ⟹   ENSRNOP00000092325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl389,157,080 - 89,244,456 (-)Ensembl
RefSeq Acc Id: NM_012924   ⟹   NP_037056
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,157,059 - 89,244,456 (-)NCBI
Rnor_6.0392,696,292 - 92,783,658 (-)NCBI
Rnor_5.0399,338,248 - 99,426,188 (-)NCBI
RGSC_v3.4388,022,962 - 88,110,352 (-)RGD
Celera388,236,830 - 88,324,125 (-)RGD
Sequence:
RefSeq Acc Id: XM_006234627   ⟹   XP_006234689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,573 (-)NCBI
Rnor_6.0392,695,083 - 92,783,820 (-)NCBI
Rnor_5.0399,338,248 - 99,426,188 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006234629   ⟹   XP_006234691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,560 (-)NCBI
Rnor_6.0392,695,083 - 92,783,816 (-)NCBI
Rnor_5.0399,338,248 - 99,426,188 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006234631   ⟹   XP_006234693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,531 (-)NCBI
Rnor_6.0392,695,083 - 92,783,800 (-)NCBI
Rnor_5.0399,338,248 - 99,426,188 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762058   ⟹   XP_008760280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,615 (-)NCBI
Rnor_6.0392,695,083 - 92,783,810 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591492   ⟹   XP_017446981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,541 (-)NCBI
Rnor_6.0392,695,083 - 92,783,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104361   ⟹   XP_038960289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,587 (-)NCBI
RefSeq Acc Id: XM_039104362   ⟹   XP_038960290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,583 (-)NCBI
RefSeq Acc Id: XM_039104363   ⟹   XP_038960291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,580 (-)NCBI
RefSeq Acc Id: XM_039104364   ⟹   XP_038960292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,578 (-)NCBI
RefSeq Acc Id: XM_039104366   ⟹   XP_038960294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,574 (-)NCBI
RefSeq Acc Id: XM_039104367   ⟹   XP_038960295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,568 (-)NCBI
RefSeq Acc Id: XM_039104368   ⟹   XP_038960296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,567 (-)NCBI
RefSeq Acc Id: XM_039104369   ⟹   XP_038960297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2389,155,850 - 89,244,524 (-)NCBI
Protein Sequences
Protein RefSeqs NP_037056 (Get FASTA)   NCBI Sequence Viewer  
  XP_006234689 (Get FASTA)   NCBI Sequence Viewer  
  XP_006234691 (Get FASTA)   NCBI Sequence Viewer  
  XP_006234693 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760280 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446981 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960289 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960290 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960291 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960292 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960294 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960295 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960296 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960297 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA53532 (Get FASTA)   NCBI Sequence Viewer  
  AAA53534 (Get FASTA)   NCBI Sequence Viewer  
  AAA92920 (Get FASTA)   NCBI Sequence Viewer  
  AAA97915 (Get FASTA)   NCBI Sequence Viewer  
  AAB54002 (Get FASTA)   NCBI Sequence Viewer  
  AAB67798 (Get FASTA)   NCBI Sequence Viewer  
  AAC17117 (Get FASTA)   NCBI Sequence Viewer  
  AAG31599 (Get FASTA)   NCBI Sequence Viewer  
  AAG31600 (Get FASTA)   NCBI Sequence Viewer  
  AAG31601 (Get FASTA)   NCBI Sequence Viewer  
  AAG31602 (Get FASTA)   NCBI Sequence Viewer  
  AAH61531 (Get FASTA)   NCBI Sequence Viewer  
  AAH85703 (Get FASTA)   NCBI Sequence Viewer  
  AAI07950 (Get FASTA)   NCBI Sequence Viewer  
  AAI27486 (Get FASTA)   NCBI Sequence Viewer  
  ACA62739 (Get FASTA)   NCBI Sequence Viewer  
  ALB05590 (Get FASTA)   NCBI Sequence Viewer  
  ALB05591 (Get FASTA)   NCBI Sequence Viewer  
  ALB05592 (Get FASTA)   NCBI Sequence Viewer  
  ALB05593 (Get FASTA)   NCBI Sequence Viewer  
  EDL79648 (Get FASTA)   NCBI Sequence Viewer  
  EDL79649 (Get FASTA)   NCBI Sequence Viewer  
  EDL79650 (Get FASTA)   NCBI Sequence Viewer  
  EDL79651 (Get FASTA)   NCBI Sequence Viewer  
  EDL79652 (Get FASTA)   NCBI Sequence Viewer  
  EDL79653 (Get FASTA)   NCBI Sequence Viewer  
  EDL79654 (Get FASTA)   NCBI Sequence Viewer  
  P26051 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037056   ⟸   NM_012924
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006234689   ⟸   XM_006234627
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006234691   ⟸   XM_006234629
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006234693   ⟸   XM_006234631
- Peptide Label: isoform X13
- UniProtKB: P26051 (UniProtKB/Swiss-Prot),   O70509 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760280   ⟸   XM_008762058
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017446981   ⟸   XM_017591492
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: ENSRNOP00000008760   ⟸   ENSRNOT00000008760
RefSeq Acc Id: ENSRNOP00000009000   ⟸   ENSRNOT00000009000
RefSeq Acc Id: ENSRNOP00000009073   ⟸   ENSRNOT00000009073
RefSeq Acc Id: XP_038960289   ⟸   XM_039104361
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960290   ⟸   XM_039104362
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038960291   ⟸   XM_039104363
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960292   ⟸   XM_039104364
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038960294   ⟸   XM_039104366
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960295   ⟸   XM_039104367
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038960296   ⟸   XM_039104368
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038960297   ⟸   XM_039104369
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000096654   ⟸   ENSRNOT00000107007
RefSeq Acc Id: ENSRNOP00000080825   ⟸   ENSRNOT00000111172
RefSeq Acc Id: ENSRNOP00000090715   ⟸   ENSRNOT00000111131
RefSeq Acc Id: ENSRNOP00000097897   ⟸   ENSRNOT00000102139
RefSeq Acc Id: ENSRNOP00000090045   ⟸   ENSRNOT00000114481
RefSeq Acc Id: ENSRNOP00000092325   ⟸   ENSRNOT00000116432
RefSeq Acc Id: ENSRNOP00000078366   ⟸   ENSRNOT00000109066
Protein Domains
Link

Transcriptome

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

Promoters
RGD ID:13692254
Promoter ID:EPDNEW_R2774
Type:multiple initiation site
Name:Cd44_1
Description:CD44 molecule
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_6.0392,783,658 - 92,783,718EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
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)
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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
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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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
F344/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
F344/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
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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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
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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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
LE/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
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)
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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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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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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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
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin