Capn3 (calpain 3) - Rat Genome Database

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Gene: Capn3 (calpain 3) Rattus norvegicus
Analyze
Symbol: Capn3
Name: calpain 3
RGD ID: 2269
Description: Enables several functions, including calcium-dependent cysteine-type endopeptidase activity; enzyme binding activity; and titin binding activity. Involved in several processes, including response to calcium ion; response to muscle activity; and sodium-dependent self proteolysis. Located in T-tubule; Z disc; and nucleus. Biomarker of hepatocellular carcinoma. Human ortholog(s) of this gene implicated in autosomal dominant limb-girdle muscular dystrophy; autosomal recessive limb-girdle muscular dystrophy type 2A; and muscular dystrophy. Orthologous to human CAPN3 (calpain 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calcium-activated neutral proteinase 3; calpain L3; calpain p94; calpain-3; CANP 3; Lp82; Lp84; Lp85; muscle-specific calcium-activated neutral protease 3; p94
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23107,407,518 - 107,457,858 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
Rnor_6.03112,227,486 - 112,278,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3112,228,720 - 112,278,408 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03118,776,357 - 118,825,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43106,946,878 - 106,998,274 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13106,843,308 - 106,894,702 (+)NCBI
Celera3106,315,875 - 106,366,640 (+)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
calcium-dependent self proteolysis  (IEA,ISO,ISS)
cellular response to calcium ion  (IEA,ISO,ISS)
cellular response to salt stress  (IEA,ISO,ISS)
G1 to G0 transition involved in cell differentiation  (IEA,ISO)
muscle structure development  (ISO,ISS)
myofibril assembly  (ISO,ISS)
negative regulation of apoptotic process  (IBA,IEA,ISO,ISS)
negative regulation of protein sumoylation  (IEA,ISO,ISS)
negative regulation of skeletal muscle cell differentiation  (ISO)
negative regulation of transcription, DNA-templated  (IEA,ISO,ISS)
positive regulation of NF-kappaB transcription factor activity  (IEA,ISO,ISS)
positive regulation of proteolysis  (IEA,ISO,ISS)
positive regulation of release of sequestered calcium ion into cytosol  (IEA,ISO,ISS)
positive regulation of satellite cell activation involved in skeletal muscle regeneration  (IEA,ISO,ISS)
positive regulation of transcription, DNA-templated  (IEA,ISO,ISS)
programmed cell death  (IEA,ISO)
protein catabolic process  (IEA,ISO,ISS)
protein destabilization  (IEA,ISO)
protein localization to membrane  (IEA,ISO,ISS)
protein-containing complex assembly  (IEA,ISO,ISS)
proteolysis  (IBA,IDA,IEA,ISO,TAS)
regulation of catalytic activity  (IEA,ISO,ISS)
regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO,ISS)
regulation of myoblast differentiation  (IEA,ISO)
response to calcium ion  (IDA)
response to muscle activity  (IDA)
response to xenobiotic stimulus  (IEP)
sarcomere organization  (IEA,ISO,ISS)
self proteolysis  (IDA,ISO)
sodium-dependent self proteolysis  (IDA)

Cellular Component
cytoplasm  (IBA,IDA,IEA,ISO)
cytosol  (IEA,ISO,ISS)
myofibril  (IDA)
nucleolus  (IEA,ISO,ISS)
nucleus  (IDA,ISO)
plasma membrane  (IDA,IEA,ISO,ISS)
protein-containing complex  (IEA,ISO,ISS)
T-tubule  (IDA)
Z disc  (IDA)

Molecular Function

References

References - curated
1. Busquets S, etal., Biochim Biophys Acta. 2000 Jun 1;1475(1):5-9.
2. Fukiage C, etal., J Biol Chem. 2002 Jun 7;277(23):20678-85. Epub 2002 Mar 19.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Guyon JR, etal., Muscle Nerve. 2003 Oct;28(4):472-83.
6. Konig N, etal., J Chem Neuroanat 2003 Feb;25(2):129-36.
7. Kramerova I, etal., Hum Mol Genet. 2008 Nov 1;17(21):3271-80. doi: 10.1093/hmg/ddn223. Epub 2008 Aug 1.
8. Ma H, etal., Exp Eye Res 1998 Aug;67(2):221-9.
9. Ma H, etal., Invest Ophthalmol Vis Sci 1998 Feb;39(2):454-61.
10. Marcilhac A, etal., Int J Biochem Cell Biol. 2006;38(12):2128-40. Epub 2006 Jul 5.
11. MGD data from the GO Consortium
12. Miyabara EH, etal., Cell Tissue Res. 2005 Mar;319(3):479-89. Epub 2005 Jan 27.
13. Murphy RM and Lamb GD, J Biol Chem. 2009 Mar 20;284(12):7811-9. doi: 10.1074/jbc.M808655200. Epub 2009 Jan 14.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. Ono Y, etal., J Biol Chem. 2010 Jul 23;285(30):22986-98. doi: 10.1074/jbc.M110.126946. Epub 2010 May 11.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Richard I, etal., Am J Hum Genet. 1997 May;60(5):1128-38.
21. Sorimachi H, etal., J Biol Chem 1989 Nov 25;264(33):20106-11.
22. Tagawa K, etal., Hum Mol Genet 2000 May 22;9(9):1393-402.
Additional References at PubMed
PMID:9642272   PMID:11120559   PMID:12482600   PMID:12658553   PMID:15138196   PMID:16107503   PMID:16857710   PMID:18073330   PMID:18310072   PMID:19295178   PMID:19386580   PMID:19556129  
PMID:20139084   PMID:20694146   PMID:23300487   PMID:23357851   PMID:26569227   PMID:29783071   PMID:34638951  


Genomics

Comparative Map Data
Capn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23107,407,518 - 107,457,858 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
Rnor_6.03112,227,486 - 112,278,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3112,228,720 - 112,278,408 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03118,776,357 - 118,825,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43106,946,878 - 106,998,274 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13106,843,308 - 106,894,702 (+)NCBI
Celera3106,315,875 - 106,366,640 (+)NCBICelera
Cytogenetic Map3q35NCBI
CAPN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1542,359,498 - 42,412,949 (+)EnsemblGRCh38hg38GRCh38
GRCh381542,359,501 - 42,412,317 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371542,651,699 - 42,704,515 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361540,427,593 - 40,491,807 (+)NCBINCBI36hg18NCBI36
Build 341540,427,592 - 40,491,807NCBI
Celera1519,408,011 - 19,472,224 (+)NCBI
Cytogenetic Map15q15.1NCBI
HuRef1519,499,872 - 19,552,636 (+)NCBIHuRef
CHM1_11542,770,186 - 42,823,000 (+)NCBICHM1_1
Capn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392120,294,074 - 120,335,400 (+)NCBIGRCm39mm39
GRCm39 Ensembl2120,294,053 - 120,335,399 (+)Ensembl
GRCm382120,463,593 - 120,504,919 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2120,456,019 - 120,504,913 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl2120,463,572 - 120,504,918 (+)EnsemblGRCm38mm10GRCm38
MGSCv372120,289,329 - 120,330,655 (+)NCBIGRCm37mm9NCBIm37
MGSCv362120,155,314 - 120,195,940 (+)NCBImm8
Celera2121,617,948 - 121,659,023 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.31NCBI
Capn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554169,070,399 - 9,117,794 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554169,070,479 - 9,121,099 (+)NCBIChiLan1.0ChiLan1.0
LOC100984344
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11539,458,400 - 39,528,820 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1539,476,302 - 39,528,820 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01521,227,371 - 21,372,406 (+)NCBIMhudiblu_PPA_v0panPan3
CAPN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1309,329,190 - 9,384,622 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl309,329,015 - 9,383,772 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha309,387,300 - 9,442,600 (+)NCBI
ROS_Cfam_1.0309,464,173 - 9,519,888 (+)NCBI
ROS_Cfam_1.0 Ensembl309,464,000 - 9,519,096 (+)Ensembl
UMICH_Zoey_3.1309,384,166 - 9,439,578 (+)NCBI
UNSW_CanFamBas_1.0309,489,492 - 9,545,424 (+)NCBI
UU_Cfam_GSD_1.0309,623,343 - 9,678,674 (+)NCBI
Capn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864087,819,711 - 87,863,585 (+)NCBI
SpeTri2.0NW_0049364715,667,839 - 5,711,822 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1128,960,121 - 129,013,547 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11128,960,117 - 129,013,508 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21143,852,337 - 143,905,767 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap1q15-q17NCBI
CAPN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12640,568,320 - 40,657,443 (-)NCBIChlSab1.1chlSab2
ChlSab1.12640,568,320 - 40,657,443 (-)NCBIChlSab1.1chlSab2
ChlSab1.12640,568,320 - 40,657,443 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2640,568,885 - 40,625,597 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666048100,380,987 - 100,442,711 (+)NCBIVero_WHO_p1.0
Capn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248049,473,075 - 9,512,643 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat261  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,411,819 - 107,412,032 (+)MAPPERmRatBN7.2
Rnor_6.03112,232,846 - 112,233,058NCBIRnor6.0
Rnor_5.03118,780,585 - 118,780,797UniSTSRnor5.0
RGSC_v3.43106,951,512 - 106,951,725RGDRGSC3.4
RGSC_v3.43106,951,513 - 106,951,725UniSTSRGSC3.4
RGSC_v3.13106,847,940 - 106,848,153RGD
Celera3106,319,855 - 106,320,067UniSTS
SHRSP x BN Map352.8698UniSTS
SHRSP x BN Map352.8698RGD
Cytogenetic Map3q35UniSTS
RH130533  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,457,515 - 107,457,712 (+)MAPPERmRatBN7.2
Rnor_6.03112,278,066 - 112,278,262NCBIRnor6.0
Rnor_5.03118,825,470 - 118,825,666UniSTSRnor5.0
RGSC_v3.43106,997,932 - 106,998,128UniSTSRGSC3.4
Celera3106,366,298 - 106,366,494UniSTS
RH 3.4 Map3940.1UniSTS
Cytogenetic Map3q35UniSTS
RH130699  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,405,888 - 107,406,075 (+)MAPPERmRatBN7.2
Rnor_6.03112,226,671 - 112,226,857NCBIRnor6.0
Rnor_5.03118,774,410 - 118,774,596UniSTSRnor5.0
RGSC_v3.43106,944,931 - 106,945,117UniSTSRGSC3.4
Celera3106,313,928 - 106,314,114UniSTS
RH 3.4 Map3939.7UniSTS
Cytogenetic Map3q35UniSTS
RH94578  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3q35UniSTS
Capn3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,408,172 - 107,408,347 (+)MAPPERmRatBN7.2
Rnor_6.03112,228,953 - 112,229,127NCBIRnor6.0
Rnor_5.03118,776,692 - 118,776,866UniSTSRnor5.0
RGSC_v3.43106,947,213 - 106,947,387UniSTSRGSC3.4
Celera3106,316,210 - 106,316,384UniSTS
Cytogenetic Map3q35UniSTS
GDB:595526  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,408,074 - 107,408,515 (+)MAPPERmRatBN7.2
Rnor_6.03112,228,855 - 112,229,295NCBIRnor6.0
Rnor_5.03118,776,594 - 118,777,034UniSTSRnor5.0
RGSC_v3.43106,947,115 - 106,947,555UniSTSRGSC3.4
Celera3106,316,112 - 106,316,552UniSTS
Cytogenetic Map3q35UniSTS
SKM-CALPOV  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,408,069 - 107,408,327 (+)MAPPERmRatBN7.2
Rnor_6.03112,228,850 - 112,229,107NCBIRnor6.0
Rnor_5.03118,776,589 - 118,776,846UniSTSRnor5.0
RGSC_v3.43106,947,110 - 106,947,367UniSTSRGSC3.4
Celera3106,316,107 - 106,316,364UniSTS
Cytogenetic Map3q35UniSTS
CANP3SKM  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,443,333 - 107,444,231 (+)MAPPERmRatBN7.2
Rnor_6.03112,263,884 - 112,264,781NCBIRnor6.0
Rnor_5.03118,811,288 - 118,812,185UniSTSRnor5.0
RGSC_v3.43106,983,750 - 106,984,647UniSTSRGSC3.4
Celera3106,352,115 - 106,353,012UniSTS
Cytogenetic Map3q35UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3102200529115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)396127817115665732Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:53
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000011761
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 8 11 8
Low 18 23 16 17 16 63 3 31 11
Below cutoff 3 25 27 18 2 18 11 32 10

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591508 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF052540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF061726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF173834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF184950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J05121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U96367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011761   ⟹   ENSRNOP00000011761
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
Rnor_6.0 Ensembl3112,228,919 - 112,278,038 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079079   ⟹   ENSRNOP00000069651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
Rnor_6.0 Ensembl3112,228,720 - 112,278,022 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080533   ⟹   ENSRNOP00000071494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,421,257 - 107,457,856 (+)Ensembl
Rnor_6.0 Ensembl3112,242,270 - 112,278,408 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082876   ⟹   ENSRNOP00000075081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,421,257 - 107,457,856 (+)Ensembl
Rnor_6.0 Ensembl3112,242,326 - 112,278,401 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108270   ⟹   ENSRNOP00000080932
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109382   ⟹   ENSRNOP00000079180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115649   ⟹   ENSRNOP00000087393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,421,257 - 107,457,856 (+)Ensembl
RefSeq Acc Id: NM_017117   ⟹   NP_058813
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,407,838 - 107,457,858 (+)NCBI
Rnor_6.03112,228,618 - 112,278,408 (+)NCBI
Rnor_5.03118,776,357 - 118,825,812 (+)NCBI
RGSC_v3.43106,946,878 - 106,998,274 (+)RGD
Celera3106,315,875 - 106,366,640 (+)RGD
Sequence:
RefSeq Acc Id: XM_006234728   ⟹   XP_006234790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,421,308 - 107,457,856 (+)NCBI
Rnor_6.03112,242,243 - 112,278,406 (+)NCBI
Rnor_5.03118,776,357 - 118,825,812 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234729   ⟹   XP_006234791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,421,264 - 107,457,856 (+)NCBI
Rnor_6.03112,242,247 - 112,278,406 (+)NCBI
Rnor_5.03118,776,357 - 118,825,812 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762081   ⟹   XP_008760303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,407,522 - 107,457,856 (+)NCBI
Rnor_6.03112,227,487 - 112,278,406 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104419   ⟹   XP_038960347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,407,521 - 107,457,856 (+)NCBI
RefSeq Acc Id: XM_039104420   ⟹   XP_038960348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,421,308 - 107,457,856 (+)NCBI
RefSeq Acc Id: XM_039104421   ⟹   XP_038960349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,407,518 - 107,457,856 (+)NCBI
RefSeq Acc Id: XM_039104422   ⟹   XP_038960350
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23107,421,266 - 107,457,856 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058813   ⟸   NM_017117
- Sequence:
RefSeq Acc Id: XP_006234791   ⟸   XM_006234729
- Peptide Label: isoform X4
- UniProtKB: O70482 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234790   ⟸   XM_006234728
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K9P9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760303   ⟸   XM_008762081
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000075081   ⟸   ENSRNOT00000082876
RefSeq Acc Id: ENSRNOP00000069651   ⟸   ENSRNOT00000079079
RefSeq Acc Id: ENSRNOP00000071494   ⟸   ENSRNOT00000080533
RefSeq Acc Id: ENSRNOP00000011761   ⟸   ENSRNOT00000011761
RefSeq Acc Id: XP_038960349   ⟸   XM_039104421
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960347   ⟸   XM_039104419
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960350   ⟸   XM_039104422
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038960348   ⟸   XM_039104420
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000080932   ⟸   ENSRNOT00000108270
RefSeq Acc Id: ENSRNOP00000079180   ⟸   ENSRNOT00000109382
RefSeq Acc Id: ENSRNOP00000087393   ⟸   ENSRNOT00000115649
Protein Domains
Calpain catalytic   EF-hand

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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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
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2269 AgrOrtholog
Ensembl Genes ENSRNOG00000008609 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011761 UniProtKB/TrEMBL
  ENSRNOP00000069651 UniProtKB/TrEMBL
  ENSRNOP00000071494 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075081 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000079180 ENTREZGENE
  ENSRNOP00000080932 ENTREZGENE
Ensembl Transcript ENSRNOT00000011761 UniProtKB/TrEMBL
  ENSRNOT00000079079 UniProtKB/TrEMBL
  ENSRNOT00000080533 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000082876 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000108270 ENTREZGENE
  ENSRNOT00000109382 ENTREZGENE
InterPro C2_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calpain_cysteine_protease UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calpain_domain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calpain_III_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAPN3/9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_cys_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C2_calpain_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29155 UniProtKB/Swiss-Prot
NCBI Gene 29155 ENTREZGENE
PANTHER PTHR10183:SF329 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Capn3 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CALPAIN_CAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THIOL_PROTEASE_CYS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CysPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49758 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JVX0_RAT UniProtKB/TrEMBL
  A0A0G2K9P9 ENTREZGENE, UniProtKB/TrEMBL
  CAN3_RAT UniProtKB/Swiss-Prot
  F1LSQ2_RAT UniProtKB/TrEMBL
  O08702_RAT UniProtKB/TrEMBL
  O70482 ENTREZGENE, UniProtKB/TrEMBL
  P16259 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Capn3  calpain 3      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the muscle, forebrain, in the corpus callosum and in the dentate gyrus of the brain 634694
gene_expression p94 isoform expressed only in skeletal muscle, not expressed in heart or in smooth muscle 69795
gene_expression Lp84 isoform expressed exclusively in lens of eye 1299839
gene_function calcium-dependent protease 634694
gene_function Lp82 isoform exhibits calcium-activated protease activity 1299852
gene_process may be involved in astrocyte plasticity and/or motility 634694
gene_process Lp82 isoform may contribute to proteolysis of lens crystallin proteins in both normal development and in cataract formation 1299852
gene_transcript alternatively spliced into p94 or Lp82 isoforms via usage of alternative exon 1 and deletions of IS1 and IS2 regions 1299839