Birc5 (baculoviral IAP repeat-containing 5) - Rat Genome Database

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Gene: Birc5 (baculoviral IAP repeat-containing 5) Rattus norvegicus
Analyze
Symbol: Birc5
Name: baculoviral IAP repeat-containing 5
RGD ID: 70499
Description: Predicted to enable several functions, including chaperone binding activity; cysteine-type endopeptidase inhibitor activity involved in apoptotic process; and protein dimerization activity. Involved in several processes, including cellular response to ethanol; cellular response to stem cell factor stimulus; and response to glucocorticoid. Located in apical plasma membrane; cytoplasm; and nucleus. Used to study endometriosis and pulmonary hypertension. Biomarker of acute pancreatitis; artery disease (multiple); congestive heart failure; high grade glioma; and stomach carcinoma. Human ortholog(s) of this gene implicated in prostate cancer and transitional cell carcinoma. Orthologous to human BIRC5 (baculoviral IAP repeat containing 5); PARTICIPATES IN histone modification pathway; colorectal cancer pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AP14; apoptosis inhibitor survivin; baculoviral IAP repeat-containing 5 (survivin); baculoviral IAP repeat-containing protein 5; survivin
RGD Orthologs
Human
Mouse
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
mRatBN7.210103,072,530 - 103,081,382 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl10103,073,408 - 103,081,380 (+)Ensembl
Rnor_6.010106,856,097 - 106,864,419 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10106,856,097 - 106,864,413 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010106,494,775 - 106,503,097 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10101,633,441 - 101,641,341 (+)NCBICelera
Cytogenetic Map10q32.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-Tetrandrine  (ISO)
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(-)-gambogic acid  (ISO)
(-)-noscapine  (ISO)
(20R)-protopanaxadiol  (ISO)
(20S)-ginsenoside Rg3  (ISO)
(S)-nicotine  (ISO)
1'-acetoxychavicol acetate  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-diaminotoluene  (ISO)
2,4-Dihydroxychalcone  (ISO)
2-acetamidofluorene  (EXP)
2-Hydroxy-6-(8,11,14-pentadecatrienyl)benzoic acid  (ISO)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (ISO)
2-trans,6-trans-farnesyl diphosphate  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,3'-diindolylmethane  (ISO)
3-iodobenzyl-5'-N-methylcarboxamidoadenosine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
3-methylcholanthrene  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-bromo-2'-deoxyuridine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acetylleucyl-leucyl-norleucinal  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alvocidib  (ISO)
amiodarone  (EXP)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
aprepitant  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (EXP)
ATP  (ISO)
atrazine  (ISO)
azadirachtin A  (ISO)
azathioprine  (ISO)
baicalein  (ISO)
barium sulfate  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
benzoic acid  (ISO)
Berbamine  (ISO)
berberine  (ISO)
beta-naphthoflavone  (EXP)
betulin  (ISO)
betulinic acid  (ISO)
bexarotene  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bleomycin A2  (ISO)
bortezomib  (ISO)
budesonide  (ISO)
buta-1,3-diene  (ISO)
butan-1-ol  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
cantharidin  (ISO)
capsaicin  (ISO)
carbon nanotube  (ISO)
celastrol  (ISO)
celecoxib  (ISO)
ceric oxide  (EXP)
chlorambucil  (ISO)
chloroquine  (ISO)
chlorpromazine  (ISO)
chrysazin  (ISO)
chrysene  (ISO)
ciclopirox  (ISO)
ciglitazone  (ISO)
Cinobufagin  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
coumarin  (ISO)
coumarins  (ISO)
coumestrol  (ISO)
crizotinib  (ISO)
crocin-1  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
dacarbazine  (ISO)
dactolisib  (ISO)
daunorubicin  (ISO)
decabromodiphenyl ether  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diallyl disulfide  (ISO)
Diallyl sulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazene  (ISO)
diazinon  (EXP,ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
dieldrin  (EXP)
digitoxin  (ISO)
dimethylarsinic acid  (EXP,ISO)
dioscin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
emodin  (ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
enzalutamide  (ISO)
enzyme inhibitor  (ISO)
epoxomicin  (ISO)
erlotinib hydrochloride  (ISO)
etacrynic acid  (ISO)
ethanol  (ISO)
etodolac  (ISO)
etoposide  (ISO)
everolimus  (ISO)
Evodiamine  (ISO)
fangchinoline  (ISO)
farnesyl diphosphate  (ISO)
fenhexamid  (ISO)
fenpyroximate  (ISO)
fisetin  (ISO)
flurbiprofen  (ISO)
folic acid  (ISO)
fucoidan  (ISO)
fulvestrant  (EXP,ISO)
furan  (EXP,ISO)
furosemide  (EXP)
gamma-aminobutyric acid  (EXP)
gamma-tocopherol  (ISO)
gedunin  (ISO)
gefitinib  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
geraniol  (ISO)
gingerol  (ISO)
glycochenodeoxycholic acid  (EXP)
guggulsterone  (ISO)
Hexamethonium  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hydroxamic acid  (ISO)
indole-3-methanol  (ISO)
indometacin  (EXP,ISO)
inuviscolide  (ISO)
irinotecan  (ISO)
isoflurane  (EXP)
isotretinoin  (ISO)
Jatrorrhizine  (ISO)
L-ascorbic acid  (ISO)
lapatinib  (ISO)
leflunomide  (ISO)
leptomycin B  (ISO)
Licochalcone A  (ISO)
Licochalcone B  (ISO)
lithium atom  (EXP)
lithium chloride  (EXP,ISO)
lithium hydride  (EXP)
lonafarnib  (ISO)
lovastatin  (ISO)
lucanthone  (ISO)
LY294002  (EXP,ISO)
magnesium oxide  (ISO)
manganese(II) chloride  (EXP)
mangiferin  (ISO)
Matrine  (ISO)
melatonin  (ISO)
melphalan  (ISO)
menadione  (ISO)
menaquinone  (ISO)
methamphetamine  (ISO)
methoxsalen  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
miconazole  (ISO)
mifepristone  (ISO)
mitomycin C  (ISO)
mitoxantrone  (ISO)
ML-7  (ISO)
monocrotaline  (EXP)
monodansylcadaverine  (ISO)
morin  (ISO)
motexafin gadolinium  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-butyl-N-(4-hydroxybutyl)nitrosamine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
naphthalene  (ISO)
navitoclax  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel ferrite  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nimesulide  (ISO)
nimodipine  (ISO)
nitric oxide  (ISO)
nitroprusside  (ISO)
nocodazole  (ISO)
o-anisidine  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
olaparib  (ISO)
oleanolic acid  (ISO)
oridonin  (ISO)
osthole  (ISO)
oxaliplatin  (EXP,ISO)
ozone  (ISO)
paclitaxel  (ISO)
palbociclib  (ISO)
palmatine  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PCB138  (ISO)
PD173074  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phytoestrogen  (ISO)
picoxystrobin  (ISO)
picropodophyllotoxin  (ISO)
pinosylvin  (ISO)
pirfenidone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
platycodin D  (ISO)
poly(I:C)  (ISO)
potassium iodide  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
prodigiosin  (ISO)
progesterone  (ISO)
propanal  (ISO)
propiconazole  (ISO)
propylparaben  (ISO)
prostaglandin E2  (ISO)
puerarin  (ISO)
pyrimidifen  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
reactive oxygen species  (ISO)
Rebamipide  (ISO)
reserpine  (ISO)
resveratrol  (EXP,ISO)
riboflavin  (ISO)
ritonavir  (ISO)
romidepsin  (ISO)
rotenone  (EXP,ISO)
Salinomycin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silibinin  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
sorafenib  (ISO)
stattic  (ISO)
staurosporine  (ISO)
sulindac  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
Tanshinone I  (ISO)
temozolomide  (ISO)
terameprocol  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thifluzamide  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
thymoquinone  (ISO)
titanium dioxide  (EXP,ISO)
tocopherol  (ISO)
Tomentosin  (ISO)
topotecan  (EXP,ISO)
trans-pinosylvin  (ISO)
triadimefon  (ISO)
Tributyltin oxide  (EXP,ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
tyrphostin AG 1478  (ISO)
tyrphostin B42  (ISO)
valproic acid  (ISO)
vemurafenib  (ISO)
venetoclax  (ISO)
verteporfin  (ISO)
vinyl carbamate  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zearalenone  (ISO)
zerumbone  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc(0)  (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. Abbate A, etal., Int J Cardiol. 2006 Aug 28;111(3):371-6. Epub 2005 Oct 27.
2. Al-Joudi FS and Iskandar ZA, Med J Malaysia. 2006 Aug;61(3):302-6.
3. Ambrosini G, etal., Nat Med 1997 Aug;3(8):917-21.
4. Athanassiadou P, etal., Pathol Res Pract. 2008;204(4):241-9. Epub 2008 Jan 2.
5. Barnes N, etal., Br J Cancer. 2006 Jan 30;94(2):253-8.
6. Brennan DJ, etal., Clin Cancer Res. 2008 May 1;14(9):2681-9.
7. Chiou SK and Mandayam S, Biochem Pharmacol. 2007 Nov 15;74(10):1485-95. Epub 2007 Jul 22.
8. Erkanli S, etal., Int J Gynecol Cancer. 2006 May-Jun;16(3):1412-8.
9. Feng ZB, etal., Zhonghua Zhong Liu Za Zhi. 2007 Sep;29(9):662-5.
10. Fukuda S, etal., J Mol Cell Cardiol. 2004 Apr;36(4):547-59.
11. Futakuchi H, etal., Int J Gynecol Cancer. 2007 Sep-Oct;17(5):1092-8.
12. Ghadersohi A, etal., Int J Cancer. 2008 Sep 15;123(6):1376-84.
13. GOA data from the GO Consortium
14. Integration of LocusLink data, October 12, 2001
15. Iskandar ZA and Al-Joudi FS, Malays J Pathol. 2006 Dec;28(2):101-5.
16. Jiao XL, etal., Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2008 Apr;16(2):294-8.
17. Jimenez LG, etal., Autoimmunity. 2007 Feb;40(1):66-72.
18. Johnson EA, etal., J Neurotrauma. 2004 Sep;21(9):1183-95.
19. Jones MK, etal., J Physiol Pharmacol. 2010 Jun;61(3):253-64.
20. Karam JA, etal., Urology. 2007 Sep;70(3):482-6.
21. Karmakar S, etal., Neurochem Res. 2007 Dec;32(12):2235-42. Epub 2007 Aug 15.
22. Koike H, etal., Urology. 2008 Mar 10;.
23. Krambeck AE, etal., Clin Cancer Res. 2007 Mar 15;13(6):1749-56.
24. Lechler P, etal., Am J Pathol. 2007 Nov;171(5):1483-98.
25. Levkau B, etal., Circulation. 2008 Mar 25;117(12):1583-93. Epub 2008 Mar 10.
26. Li ZD, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2009 Jun;29(6):1141-3.
27. Liu JR, etal., Pathol Res Pract. 2015 Jun;211(6):426-34. doi: 10.1016/j.prp.2015.01.007. Epub 2015 Jan 24.
28. Lu N, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2007 Dec;27(12):1856-9.
29. Mahotka C, etal., Int J Cancer. 2002 Jul 1;100(1):30-6.
30. Marsillach J, etal., Mol Cell Biochem. 2008 Jan;308(1-2):101-9. Epub 2007 Oct 16.
31. McMurtry MS, etal., J Clin Invest. 2005 Jun;115(6):1479-91.
32. MGD data from the GO Consortium
33. Nakahara T, etal., Cancer Res. 2007 Sep 1;67(17):8014-21.
34. Nassar A, etal., Appl Immunohistochem Mol Morphol. 2008 Mar;16(2):113-20.
35. NCBI rat LocusLink and RefSeq merged data July 26, 2002
36. Oishi Y, etal., J Hum Genet. 2007;52(3):271-9. Epub 2007 Feb 7.
37. Okazaki T, etal., Neurosci Lett. 2008 Jan 10;430(2):109-14. Epub 2007 Nov 6.
38. Ozisik K, etal., Transplant Proc. 2006 Nov;38(9):2784-7.
39. Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
40. Pina-Cabral L, etal., Clin Transl Oncol. 2007 Nov;9(11):731-6.
41. Pipeline to import KEGG annotations from KEGG into RGD
42. RGD automated data pipeline
43. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
44. RGD automated import pipeline for gene-chemical interactions
45. RGD comprehensive gene curation
46. Singh RP, etal., Clin Cancer Res. 2008 Jan 1;14(1):300-8.
47. Sommer KW, etal., Oncogene 2003 Jul 3;22(27):4266-80.
48. Takamizawa S, etal., J Pediatr Surg. 2001 Jan;36(1):37-42.
49. Tashiro M, etal., Pancreas. 2003 Mar;26(2):160-5.
50. Tyagi A, etal., Mol Cancer Ther. 2007 Dec;6(12 Pt 1):3248-55.
51. Wang Y, etal., J Huazhong Univ Sci Technolog Med Sci. 2007 Aug;27(4):444-7.
52. Wang Y, etal., Mol Cell Endocrinol. 2004 Apr 15;218(1-2):165-74.
53. Wei SB, etal., Zhongguo Zhong Xi Yi Jie He Za Zhi. 2008 Feb;28(2):139-41.
54. Yi L, etal., Onkologie. 2007 Oct;30(10):502-6. Epub 2007 Sep 21.
55. Yie SM, etal., Clin Exp Metastasis. 2006;23(5-6):279-89. Epub 2006 Nov 3.
56. Yin RT, etal., Sichuan Da Xue Xue Bao Yi Xue Ban. 2007 Mar;38(2):243-5.
57. Zhu XD, etal., World J Gastroenterol. 2003 Jul;9(7):1435-8.
58. Ziaee SA, etal., Urol J. 2006 Summer;3(3):150-3.
Additional References at PubMed
PMID:9859993   PMID:10626797   PMID:10876248   PMID:10949039   PMID:11069302   PMID:11084331   PMID:11516652   PMID:12679106   PMID:12773388   PMID:12805209   PMID:15260989   PMID:15665297  
PMID:16049172   PMID:16239925   PMID:16291752   PMID:16322459   PMID:17099693   PMID:17428462   PMID:18086682   PMID:18358624   PMID:18591255   PMID:19018973   PMID:19035263   PMID:19073407  
PMID:19576024   PMID:19644667   PMID:20514400   PMID:20564420   PMID:20627126   PMID:20826784   PMID:20887644   PMID:21252625   PMID:21364656   PMID:21536684   PMID:21706383   PMID:21708067  
PMID:21976248   PMID:22139302   PMID:22819929   PMID:22883038   PMID:23251006   PMID:23658701   PMID:23884942   PMID:24935577   PMID:25318914   PMID:25323860   PMID:25539851   PMID:25744839  
PMID:25778398   PMID:25816072   PMID:25843524   PMID:25856227   PMID:26347229   PMID:26464661   PMID:26818429   PMID:27046449   PMID:27539959   PMID:28218735   PMID:30251448  


Genomics

Comparative Map Data
Birc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210103,072,530 - 103,081,382 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl10103,073,408 - 103,081,380 (+)Ensembl
Rnor_6.010106,856,097 - 106,864,419 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10106,856,097 - 106,864,413 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010106,494,775 - 106,503,097 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10101,633,441 - 101,641,341 (+)NCBICelera
Cytogenetic Map10q32.2NCBI
BIRC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1778,214,186 - 78,225,636 (+)EnsemblGRCh38hg38GRCh38
GRCh381778,214,253 - 78,225,635 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371776,210,334 - 76,221,716 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361773,721,872 - 73,733,311 (+)NCBINCBI36hg18NCBI36
Build 341773,721,871 - 73,733,310NCBI
Celera1772,806,306 - 72,817,744 (+)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1771,634,433 - 71,645,847 (+)NCBIHuRef
CHM1_11776,274,801 - 76,286,240 (+)NCBICHM1_1
Birc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911117,740,063 - 117,746,569 (+)NCBIGRCm39mm39
GRCm39 Ensembl11117,740,077 - 117,746,569 (+)Ensembl
GRCm3811117,849,237 - 117,855,743 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11117,849,251 - 117,855,743 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711117,710,551 - 117,717,057 (+)NCBIGRCm37mm9NCBIm37
MGSCv3611117,665,327 - 117,671,833 (+)NCBImm8
Celera11129,594,259 - 129,600,765 (+)NCBICelera
Cytogenetic Map11E2NCBI
BIRC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11777,842,724 - 77,854,159 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1777,842,724 - 77,854,159 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01772,292,332 - 72,303,493 (+)NCBIMhudiblu_PPA_v0panPan3
BIRC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.192,930,308 - 2,959,307 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha93,613,921 - 3,619,074 (-)NCBI
ROS_Cfam_1.093,608,303 - 3,613,418 (-)NCBI
UMICH_Zoey_3.193,631,386 - 3,636,494 (-)NCBI
UNSW_CanFamBas_1.093,755,584 - 3,761,556 (-)NCBI
UU_Cfam_GSD_1.093,836,949 - 3,842,103 (-)NCBI
Birc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056023,591,620 - 3,599,727 (-)NCBI
SpeTri2.0NW_0049365942,812,165 - 2,820,618 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BIRC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl123,747,237 - 3,755,188 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1123,747,276 - 3,755,214 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
BIRC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11670,226,824 - 70,237,000 (+)NCBI
Vero_WHO_p1.0NW_02366607741,335,707 - 41,347,619 (+)NCBI
Birc5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248017,727,084 - 7,735,946 (+)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:434
Count of miRNA genes:240
Interacting mature miRNAs:286
Transcripts:ENSRNOT00000072387
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 33 26 17 26 53 21 37
Low 15 24 15 2 15 4 7 21 14 4 11 4
Below cutoff 2 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072387   ⟹   ENSRNOP00000065784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10103,073,408 - 103,081,380 (+)Ensembl
Rnor_6.0 Ensembl10106,856,097 - 106,864,413 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096623   ⟹   ENSRNOP00000076513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10103,073,408 - 103,078,854 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106040   ⟹   ENSRNOP00000095300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10103,073,476 - 103,081,380 (+)Ensembl
RefSeq Acc Id: NM_022274   ⟹   NP_071610
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,073,459 - 103,081,382 (+)NCBI
Rnor_6.010106,856,097 - 106,864,419 (+)NCBI
Rnor_5.010106,494,775 - 106,503,097 (+)NCBI
Celera10101,633,441 - 101,641,341 (+)RGD
Sequence:
RefSeq Acc Id: XM_039086783   ⟹   XP_038942711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,072,530 - 103,081,382 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_071610   ⟸   NM_022274
- Sequence:
RefSeq Acc Id: ENSRNOP00000065784   ⟸   ENSRNOT00000072387
RefSeq Acc Id: XP_038942711   ⟸   XM_039086783
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000076513   ⟸   ENSRNOT00000096623
RefSeq Acc Id: ENSRNOP00000095300   ⟸   ENSRNOT00000106040

Transcriptome

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

Promoters
RGD ID:13697934
Promoter ID:EPDNEW_R8459
Type:multiple initiation site
Name:Birc5_1
Description:baculoviral IAP repeat-containing 5
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_6.010106,856,074 - 106,856,134EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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)
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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
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)
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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
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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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