Vim (vimentin) - Rat Genome Database
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Gene: Vim (vimentin) Rattus norvegicus
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Symbol: Vim
Name: vimentin
RGD ID: 621646
Description: Exhibits protein kinase binding activity and protein phosphatase 2A binding activity. Involved in several processes, including decidualization; regulation of neurogenesis; and response to vitamin D. Localizes to several cellular components, including axon; cell body; and perinuclear region of cytoplasm. Biomarker of Chagas disease; cerebral infarction; hyperthyroidism; nephrosis; and pulmonary hypertension. Human ortholog(s) of this gene implicated in atherosclerosis; autoimmune disease (multiple); and cataract 30. Orthologous to human VIM (vimentin); PARTICIPATES IN cyclooxygenase mediated pathway of arachidonic acid metabolism; INTERACTS WITH (R)-carnitine; 1,3-dinitrobenzene; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01780,882,715 - 80,891,200 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1780,882,666 - 80,891,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01782,500,898 - 82,509,383 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,847,280 - 87,855,763 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,858,112 - 87,866,596 (+)NCBI
Celera1776,037,845 - 76,046,329 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-citrinin  (ISO)
(20S)-ginsenoside Rg3  (ISO)
(R)-carnitine  (EXP)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,3-dinitrobenzene  (EXP)
1-naphthyl isothiocyanate  (EXP)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,5-hexanedione  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
2-methyl-2-[4-(1,2,3,4-tetrahydronaphthalen-1-yl)phenoxy]propanoic acid  (EXP)
2-naphthylamine  (ISO)
2-nitrofluorene  (EXP)
2-Oxohexane  (ISO)
3',5'-cyclic GMP  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,4-dihydroxybenzaldehyde  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroperoxycyclophosphamide  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (EXP,ISO)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
6-Cyano-7-nitroquinoxaline-2,3-dione  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
acetylcholine  (ISO)
acrolein  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
aluminium atom  (ISO)
aluminium(0)  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
andrographolide  (ISO)
anthocyanin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arecoline  (ISO)
aristolochic acid  (EXP,ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
atrazine  (ISO)
bacitracin  (EXP)
bafilomycin A1  (ISO)
bathocuproine disulfonic acid  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
Brodifacoum  (EXP)
bucladesine  (ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
calyculin a  (EXP)
cannabidiol  (ISO)
capsaicin  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP)
carvedilol  (EXP)
casticin  (ISO)
CHIR 99021  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clodronic acid  (EXP)
clofibrate  (EXP)
clofibric acid  (EXP)
cobalt dichloride  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
coumarin  (ISO)
crizotinib  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
cypermethrin  (EXP,ISO)
D-glucose  (ISO)
dantrolene  (EXP)
daunorubicin  (EXP)
DDE  (EXP)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
Deguelin  (ISO)
Deoxyschizandrin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
Di-n-octyl phthalate  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dichromium trioxide  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
Dictamnine  (ISO)
dieckol  (ISO)
diethylstilbestrol  (ISO)
dihydroartemisinin  (ISO)
dioxygen  (EXP,ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP,ISO)
emodin  (EXP)
endosulfan  (EXP,ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ergosta-4,6,8(14),22-tetraen-3-one  (ISO)
ethanol  (EXP)
ethyl methanesulfonate  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
everolimus  (ISO)
fenamidone  (ISO)
fentin chloride  (ISO)
finasteride  (EXP)
fisetin  (ISO)
flavonol  (ISO)
fluvastatin  (EXP)
folic acid  (ISO)
folpet  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
GW 6471  (EXP)
heptachlor  (ISO)
hexane  (ISO)
homocysteine  (EXP)
hyaluronic acid  (EXP,ISO)
hydrogen peroxide  (EXP,ISO)
hydrogen sulfide  (ISO)
indole-3-methanol  (ISO)
indometacin  (EXP,ISO)
ionomycin  (ISO)
isoprenaline  (ISO)
jaspamide  (ISO)
ketoconazole  (EXP)
KN-93  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lapatinib  (ISO)
lead diacetate  (ISO)
lead(II) chloride  (ISO)
leflunomide  (EXP)
levofloxacin  (EXP)
limonin  (ISO)
linsidomine  (EXP)
lipopolysaccharide  (ISO)
lithium chloride  (EXP,ISO)
losartan  (ISO)
lutein  (ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP)
mangiferin  (ISO)
medroxyprogesterone acetate  (ISO)
menadione  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
methylmercury chloride  (EXP,ISO)
methylseleninic acid  (ISO)
microcystin-LR  (EXP,ISO)
mifepristone  (ISO)
MK-2206  (EXP)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (ISO)
monocrotaline  (EXP)
morphine  (EXP)
morusin  (ISO)
N(6)-dimethylallyladenine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nafenopin  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel subsulfide  (EXP)
Niclosamide  (ISO)
nicotine  (ISO)
nifedipine  (EXP)
nimesulide  (EXP)
nitrogen mustard  (ISO)
Nonylphenol  (EXP,ISO)
nystatin  (ISO)
ochratoxin A  (EXP,ISO)
oridonin  (ISO)
oxcarbazepine  (EXP)
oxycodone  (EXP)
ozone  (EXP)
Pachymic acid  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP,ISO)
phenol red  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
poly(guanylic acid)  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
pyrogallol  (ISO)
pyrrolidine dithiocarbamate  (EXP,ISO)
pyrvinium  (ISO)
quercetin  (EXP,ISO)
Rebamipide  (EXP)
resveratrol  (EXP,ISO)
rosmarinic acid  (EXP)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (EXP)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
Salinomycin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (EXP,ISO)
serpentine asbestos  (ISO)
silibinin  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (EXP,ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
sodium fluoride  (EXP)
sodium hydrogencarbonate  (EXP)
Soman  (EXP)
sorafenib  (ISO)
staurosporine  (EXP)
streptozocin  (EXP)
sulfasalazine  (ISO)
sulforaphane  (EXP,ISO)
Swertiamarin  (EXP)
tacrolimus hydrate  (ISO)
tamibarotene  (ISO)
Tanshinone I  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetraethylenepentamine  (ISO)
thioacetamide  (EXP,ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
topotecan  (ISO)
toxaphene  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
trichostatin A  (EXP,ISO)
triclosan  (ISO)
triphenylstannane  (ISO)
tyrphostin AG 1478  (ISO)
U-73122  (EXP)
undecane  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (EXP,ISO)
verapamil  (EXP)
vinclozolin  (EXP)
vorinostat  (ISO)
warfarin  (ISO)
wortmannin  (ISO)
XAV939  (ISO)
Y-27632  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Akoglu T, etal., Clin Immunol Immunopathol. 1986 Dec;41(3):427-32.
2. Avola R, etal., Clin Exp Hypertens. 2004 May;26(4):323-33.
3. Baldwin SA and Scheff SW, Glia. 1996 Mar;16(3):266-75.
4. Bartel-Friedrich S, etal., Anticancer Res. 2007 Jul-Aug;27(4A):2059-69.
5. Bechtold DA and Brown IR, Neurochem Res 2003 Aug;28(8):1163-73.
6. Biaggio VS, etal., Br J Nutr. 2011 Oct 12:1-9.
7. Bussemakers MJ, etal., Biochem Biophys Res Commun 1992 Feb 14;182(3):1254-9.
8. Bussemakers MJ, etal., Biochem Biophys Res Commun 1992 Jan 15;182(1):318-24.
9. Chang IA, etal., FASEB J. 2012 Feb 27.
10. Chen YM, etal., Biol Reprod. 2003 Aug;69(2):656-72. Epub 2003 Apr 16.
11. Cheng TJ, etal., J Cell Biochem. 2000 Jul 19;79(1):126-38.
12. Cizkova D, etal., Histochem Cell Biol. 2009 Feb;131(2):197-206. Epub 2008 Oct 22.
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14. El-Barbary AM, etal., J Rheumatol. 2011 May;38(5):828-34. Epub 2011 Mar 1.
15. Erkekoglu P, etal., Arch Environ Contam Toxicol. 2012 Apr;62(3):539-47. Epub 2011 Oct 16.
16. Franch A, etal., J Rheumatol. 1994 Mar;21(3):489-97.
17. GOA data from the GO Consortium
18. Graf M, etal., Hum Reprod. 2011 Jan;26(1):59-66. doi: 10.1093/humrep/deq319. Epub 2010 Nov 26.
19. Kelso ML, etal., Neuroscience. 2011 Dec 1;197:381-93. Epub 2011 Sep 16.
20. Korgun ET, etal., J Mol Histol. 2007 Aug;38(4):253-60. Epub 2007 May 22.
21. Korzhevskii DE, etal., Neurosci Behav Physiol. 2008 Oct;38(8):845-8. Epub 2008 Sep 18.
22. Kurki P, etal., J Rheumatol. 1983 Aug;10(4):558-62.
23. Lau AS and Mruk DD, Endocrinology. 2003 Apr;144(4):1549-63.
24. Levin EC, etal., Brain Res. 2009 Nov 17;1298:194-207. Epub 2009 Sep 1.
25. Lin J and Cai W, J Neurotrauma. 2004 Nov;21(11):1671-82.
26. MGD data from the GO Consortium
27. Moon C, etal., Brain Res. 2004 Dec 3;1028(2):238-42.
28. Nakamura Y, etal., Int J Cancer. 2009 Jun 1;124(11):2512-9.
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. Niknami M, etal., Int J Biochem Cell Biol. 2009 May;41(5):994-7. doi: 10.1016/j.biocel.2008.07.017. Epub 2008 Aug 8.
31. OMIM Disease Annotation Pipeline
32. Pekny M, etal., J Cell Biol. 1999 May 3;145(3):503-14.
33. Poduri A, etal., Mol Cell Biochem. 2012 Jan;360(1-2):181-8. Epub 2011 Sep 22.
34. Ranchoux B, etal., Circulation. 2015 Mar 17;131(11):1006-18. doi: 10.1161/CIRCULATIONAHA.114.008750. Epub 2015 Jan 15.
35. RGD automated data pipeline
36. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. RGD automated import pipeline for gene-chemical interactions
38. Roymans D, etal., Exp Cell Res. 2000 Nov 25;261(1):127-38.
39. Shapiro F, etal., Anat Rec. 1995 Jan;241(1):39-48.
40. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
41. Teichert-Kuliszewska K, etal., Int J Obes Relat Metab Disord. 1996 Mar;20 Suppl 3:S108-13.
42. Toth C, etal., PLoS ONE. 2008 Apr 23;3(4):e2014.
43. Toyooka T, etal., J Neurotrauma. 2011 Apr;28(4):607-18. Epub 2011 Mar 24.
44. Upadhyay R, etal., Histochem Cell Biol. 2011 Nov;136(5):543-55. Epub 2011 Sep 14.
45. van de Stadt LA, etal., Arthritis Rheum. 2011 Nov;63(11):3226-33. doi: 10.1002/art.30537.
46. Wen JJ and Garg NJ, Mol Cell Proteomics. 2011 Dec 22.
47. Zamoner A, etal., Mol Cell Endocrinol. 2007 Mar 15;267(1-2):116-26. Epub 2007 Jan 20.
48. Zamoner A, etal., Steroids. 2008 Dec 22;73(14):1400-8. Epub 2008 Jul 17.
49. Zou J, etal., Virchows Arch. 2006 Apr;448(4):485-92. Epub 2006 Jan 18.
Additional References at PubMed
PMID:2493000   PMID:8188282   PMID:9150946   PMID:9305626   PMID:10625659   PMID:10816608   PMID:10852826   PMID:10989258   PMID:11487638   PMID:11889032   PMID:12177195   PMID:12244133  
PMID:12496370   PMID:12819359   PMID:14681019   PMID:14760703   PMID:15037121   PMID:15383276   PMID:15389538   PMID:15489334   PMID:15748847   PMID:15846844   PMID:15958512   PMID:15965470  
PMID:16052496   PMID:16128803   PMID:16169070   PMID:16493181   PMID:16629905   PMID:16769727   PMID:17050693   PMID:17485853   PMID:17881773   PMID:17882221   PMID:18178558   PMID:18198667  
PMID:18316471   PMID:18577232   PMID:19144319   PMID:19182904   PMID:19223297   PMID:19241870   PMID:19420356   PMID:19726676   PMID:20015863   PMID:20103531   PMID:20131911   PMID:20427712  
PMID:20458337   PMID:20479526   PMID:20603131   PMID:20617137   PMID:21139996   PMID:21245955   PMID:21266579   PMID:21343257   PMID:21362503   PMID:21423176   PMID:21426942   PMID:21746880  
PMID:21900206   PMID:21914078   PMID:22005459   PMID:22082260   PMID:22357929   PMID:22869704   PMID:22871113   PMID:22952236   PMID:23106098   PMID:23239537   PMID:23390484   PMID:23979707  
PMID:24057876   PMID:24728265   PMID:24874717   PMID:26170015   PMID:26377600   PMID:27021728   PMID:27335427   PMID:27812135   PMID:27919618   PMID:28169954   PMID:28705472   PMID:29476059  
PMID:29496907   PMID:29803674   PMID:31626376   PMID:31904090  


Genomics

Comparative Map Data
Vim
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01780,882,715 - 80,891,200 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1780,882,666 - 80,891,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01782,500,898 - 82,509,383 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,847,280 - 87,855,763 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,858,112 - 87,866,596 (+)NCBI
Celera1776,037,845 - 76,046,329 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
VIM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1017,228,241 - 17,237,593 (+)EnsemblGRCh38hg38GRCh38
GRCh381017,228,241 - 17,237,593 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371017,269,934 - 17,279,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361017,311,304 - 17,319,598 (+)NCBINCBI36hg18NCBI36
Build 341017,311,308 - 17,319,594NCBI
Celera1017,203,520 - 17,212,854 (+)NCBI
Cytogenetic Map10p13NCBI
HuRef1017,183,488 - 17,192,823 (+)NCBIHuRef
CHM1_11017,270,372 - 17,279,705 (+)NCBICHM1_1
Vim
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39213,579,122 - 13,587,637 (+)NCBIGRCm39mm39
GRCm38213,574,311 - 13,582,826 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,573,927 - 13,582,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv37213,495,938 - 13,504,453 (+)NCBIGRCm37mm9NCBIm37
MGSCv36213,491,805 - 13,500,660 (+)NCBImm8
Celera213,484,803 - 13,493,320 (+)NCBICelera
Cytogenetic Map2A1NCBI
cM Map210.04NCBI
Vim
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,707,719 - 10,717,554 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,708,852 - 10,716,743 (-)NCBIChiLan1.0ChiLan1.0
VIM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11017,818,285 - 17,826,642 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1017,818,285 - 17,826,642 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01017,546,389 - 17,554,702 (+)NCBIMhudiblu_PPA_v0panPan3
VIM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl219,671,316 - 19,679,466 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1219,671,316 - 19,679,367 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Vim
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493652010,051,692 - 10,059,324 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VIM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1043,517,307 - 43,526,172 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11043,516,441 - 43,526,172 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21048,225,950 - 48,235,670 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VIM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl917,183,388 - 17,191,829 (+)Ensembl
ChlSab1.1917,183,466 - 17,191,771 (+)NCBI
Vim
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479610,624,672 - 10,632,300 (-)NCBI

Position Markers
RH138541  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,881,948 - 80,882,097NCBIRnor6.0
Rnor_5.01782,500,131 - 82,500,280UniSTSRnor5.0
RGSC_v3.41787,846,513 - 87,846,662UniSTSRGSC3.4
Celera1776,037,078 - 76,037,227UniSTS
Cytogenetic Map17q12.3UniSTS
RH 3.4 Map17773.0UniSTS
MARC_31619-31620:1062167711:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,888,613 - 80,889,184NCBIRnor6.0
Rnor_5.01782,506,797 - 82,507,367UniSTSRnor5.0
RGSC_v3.41787,853,178 - 87,853,747UniSTSRGSC3.4
Celera1776,043,743 - 76,044,313UniSTS
Cytogenetic Map17q12.3UniSTS
VIM  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,886,829 - 80,887,036NCBIRnor6.0
Rnor_5.01782,505,012 - 82,505,219UniSTSRnor5.0
RGSC_v3.41787,851,394 - 87,851,601UniSTSRGSC3.4
Celera1776,041,959 - 76,042,166UniSTS
Cytogenetic Map17q12.3UniSTS
VIM  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,886,820 - 80,887,069NCBIRnor6.0
Rnor_5.01782,505,003 - 82,505,252UniSTSRnor5.0
RGSC_v3.41787,851,385 - 87,851,634UniSTSRGSC3.4
Celera1776,041,950 - 76,042,199UniSTS
Cytogenetic Map17q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177485263085183543Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177570542786731080Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mirlet7drno-let-7d-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir223rno-miR-223-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mirlet7brno-let-7b-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mirlet7a1rno-let-7a-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir382rno-miR-382-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir320arno-miR-320-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir138-2rno-miR-138-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mirlet7irno-let-7i-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mirlet7c1rno-let-7c-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir185rno-miR-185-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir129-2rno-miR-129-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000024430
Prediction methods:Miranda, Rnahybrid
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 8 14 16 2
Medium 3 35 57 41 19 41 8 11 60 35 25 9 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024430   ⟹   ENSRNOP00000024430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1780,882,666 - 80,891,212 (+)Ensembl
RefSeq Acc Id: NM_031140   ⟹   NP_112402
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01780,882,715 - 80,891,200 (+)NCBI
Rnor_5.01782,500,898 - 82,509,383 (+)NCBI
RGSC_v3.41787,847,280 - 87,855,763 (+)RGD
Celera1776,037,845 - 76,046,329 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112402   ⟸   NM_031140
- UniProtKB: P31000 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024430   ⟸   ENSRNOT00000024430
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13700597
Promoter ID:EPDNEW_R11120
Type:multiple initiation site
Name:Vim_1
Description:vimentin
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_6.01780,882,664 - 80,882,724EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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
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/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
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 (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
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
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
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
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 (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
SBH/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: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621646 AgrOrtholog
Ensembl Genes ENSRNOG00000018087 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024430 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024430 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.1160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5621065 IMAGE-MGC_LOAD
InterPro IF_conserved UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom_coil1B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vimentin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81818 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72372 IMAGE-MGC_LOAD
NCBI Gene 81818 ENTREZGENE
PANTHER PTHR45652:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Filament_head UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vim PhenoGen
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.2710 ENTREZGENE
UniProt G3V8C3_RAT UniProtKB/TrEMBL
  P31000 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Vim  vimentin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Vim  vimentin      Symbol and Name status set to provisional 70820 PROVISIONAL