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 and Z disc. 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
Previously 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
GRCr83127,860,002 - 127,913,677 (+)NCBIGRCr8
mRatBN7.23107,407,518 - 107,457,858 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3111,082,641 - 111,132,438 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03119,678,209 - 119,728,005 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03117,338,596 - 117,388,398 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Calpain-3 gene expression is decreased during experimental cancer cachexia. Busquets S, etal., Biochim Biophys Acta. 2000 Jun 1;1475(1):5-9.
2. Characterization and regulation of lens-specific calpain Lp82. Fukiage C, etal., J Biol Chem. 2002 Jun 7;277(23):20678-85. Epub 2002 Mar 19.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Calpain 3 cleaves filamin C and regulates its ability to interact with gamma- and delta-sarcoglycans. Guyon JR, etal., Muscle Nerve. 2003 Oct;28(4):472-83.
6. Calpain 3 is expressed in astrocytes of rat and Microcebus brain. Konig N, etal., J Chem Neuroanat 2003 Feb;25(2):129-36.
7. Novel role of calpain-3 in the triad-associated protein complex regulating calcium release in skeletal muscle. Kramerova I, etal., Hum Mol Genet. 2008 Nov 1;17(21):3271-80. doi: 10.1093/hmg/ddn223. Epub 2008 Aug 1.
8. Protein for Lp82 calpain is expressed and enzymatically active in young rat lens. Ma H, etal., Exp Eye Res 1998 Aug;67(2):221-9.
9. Cloning and expression of mRNA for calpain Lp82 from rat lens: splice variant of p94. Ma H, etal., Invest Ophthalmol Vis Sci 1998 Feb;39(2):454-61.
10. Detection and localization of calpain 3-like protease in a neuronal cell line: possible regulation of apoptotic cell death through degradation of nuclear IkappaBalpha. Marcilhac A, etal., Int J Biochem Cell Biol. 2006;38(12):2128-40. Epub 2006 Jul 5.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. Expression of tropism-related genes in regenerating skeletal muscle of rats treated with cyclosporin-A. Miyabara EH, etal., Cell Tissue Res. 2005 Mar;319(3):479-89. Epub 2005 Jan 27.
13. Endogenous calpain-3 activation is primarily governed by small increases in resting cytoplasmic [Ca2+] and is not dependent on stretch. 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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. Skeletal muscle-specific calpain is an intracellular Na+-dependent protease. Ono Y, etal., J Biol Chem. 2010 Jul 23;285(30):22986-98. doi: 10.1074/jbc.M110.126946. Epub 2010 May 11.
17. GOA pipeline RGD automated data pipeline
18. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Multiple independent molecular etiology for limb-girdle muscular dystrophy type 2A patients from various geographical origins. Richard I, etal., Am J Hum Genet. 1997 May;60(5):1128-38.
21. Molecular cloning of a novel mammalian calcium-dependent protease distinct from both m- and mu-types. Specific expression of the mRNA in skeletal muscle. Sorimachi H, etal., J Biol Chem 1989 Nov 25;264(33):20106-11.
22. Myopathy phenotype of transgenic mice expressing active site-mutated inactive p94 skeletal muscle-specific calpain, the gene product responsible for limb girdle muscular dystrophy type 2A. 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
GRCr83127,860,002 - 127,913,677 (+)NCBIGRCr8
mRatBN7.23107,407,518 - 107,457,858 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3111,082,641 - 111,132,438 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03119,678,209 - 119,728,005 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03117,338,596 - 117,388,398 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381542,359,501 - 42,412,317 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1542,359,498 - 42,412,949 (+)EnsemblGRCh38hg38GRCh38
GRCh371542,651,699 - 42,704,515 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361540,427,593 - 40,491,807 (+)NCBINCBI36Build 36hg18NCBI36
Build 341540,427,592 - 40,491,807NCBI
Celera1519,408,011 - 19,472,224 (+)NCBICelera
Cytogenetic Map15q15.1NCBI
HuRef1519,499,872 - 19,552,636 (+)NCBIHuRef
CHM1_11542,770,186 - 42,823,000 (+)NCBICHM1_1
T2T-CHM13v2.01540,165,536 - 40,218,365 (+)NCBIT2T-CHM13v2.0
Capn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392120,294,074 - 120,335,400 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2120,294,053 - 120,335,399 (+)EnsemblGRCm39 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 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362120,155,314 - 120,195,940 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v21631,516,778 - 31,661,908 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11535,671,129 - 35,815,136 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01521,227,371 - 21,372,406 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11539,458,400 - 39,528,820 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1539,386,377 - 39,468,956 (+)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl1539,476,302 - 39,528,820 (+)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0309,464,173 - 9,519,888 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl309,464,000 - 9,519,096 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1309,384,166 - 9,439,578 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0309,489,492 - 9,545,424 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0309,623,343 - 9,678,674 (+)NCBIUU_Cfam_GSD_1.0
Capn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864087,819,711 - 87,863,585 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364715,668,169 - 5,711,075 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364715,667,839 - 5,711,822 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1128,960,118 - 129,013,546 (-)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2640,568,885 - 40,625,597 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048100,380,987 - 100,442,711 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248049,473,117 - 9,512,353 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248049,473,075 - 9,512,643 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Capn3
200 total Variants
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.


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

Markers in Region
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 Map352.8698RGD
SHRSP x BN Map352.8698UniSTS
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


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_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_039104421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283197 (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
  JAXUCZ010000003 (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
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
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
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109382   ⟹   ENSRNOP00000079180
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,407,850 - 107,457,858 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115649   ⟹   ENSRNOP00000087393
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
GRCr83127,861,590 - 127,911,607 (+)NCBI
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_006234729   ⟹   XP_006234791
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,875,058 - 127,913,677 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,861,212 - 127,913,677 (+)NCBI
mRatBN7.23107,407,522 - 107,457,856 (+)NCBI
Rnor_6.03112,227,487 - 112,278,406 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104421   ⟹   XP_038960349
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,860,002 - 127,913,677 (+)NCBI
mRatBN7.23107,407,518 - 107,457,856 (+)NCBI
RefSeq Acc Id: XM_039104422   ⟹   XP_038960350
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,875,058 - 127,913,677 (+)NCBI
mRatBN7.23107,421,266 - 107,457,856 (+)NCBI
RefSeq Acc Id: XM_063283197   ⟹   XP_063139267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,860,002 - 127,913,677 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_058813   ⟸   NM_017117
- UniProtKB: P16259 (UniProtKB/Swiss-Prot),   A0A8I5ZRY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234791   ⟸   XM_006234729
- Peptide Label: isoform X4
- UniProtKB: O70482 (UniProtKB/TrEMBL),   Q9QZF9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760303   ⟸   XM_008762081
- Peptide Label: isoform X2
- UniProtKB: F1LSQ2 (UniProtKB/TrEMBL)
- 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 X3
- UniProtKB: A0A8I5ZMW7 (UniProtKB/TrEMBL),   F1LSQ2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960350   ⟸   XM_039104422
- Peptide Label: isoform X5
- UniProtKB: O08702 (UniProtKB/TrEMBL),   A0A0G2K0L5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000080932   ⟸   ENSRNOT00000108270
RefSeq Acc Id: ENSRNOP00000079180   ⟸   ENSRNOT00000109382
RefSeq Acc Id: ENSRNOP00000087393   ⟸   ENSRNOT00000115649
RefSeq Acc Id: XP_063139267   ⟸   XM_063283197
- Peptide Label: isoform X1
Protein Domains
Calpain catalytic   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P16259-F1-model_v2 AlphaFold P16259 1-821 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2269 AgrOrtholog
BioCyc Gene G2FUF-48164 BioCyc
Ensembl Genes ENSRNOG00000008609 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011761.7 UniProtKB/TrEMBL
  ENSRNOT00000079079.2 UniProtKB/TrEMBL
  ENSRNOT00000080533.2 UniProtKB/TrEMBL
  ENSRNOT00000082876.2 UniProtKB/TrEMBL
  ENSRNOT00000108270 ENTREZGENE
  ENSRNOT00000108270.1 UniProtKB/TrEMBL
  ENSRNOT00000109382.1 UniProtKB/TrEMBL
  ENSRNOT00000115649.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.380 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 CALPAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10183:SF329 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calpain_u2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_6 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
RatGTEx ENSRNOG00000008609 RatGTEx
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
  A0A0G2K0L5 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K9P9_RAT UniProtKB/TrEMBL
  A0A8I5ZMW7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZRY1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A336_RAT UniProtKB/TrEMBL
  A6HPJ0_RAT UniProtKB/TrEMBL
  A6HPJ1_RAT UniProtKB/TrEMBL
  A6HPJ2_RAT UniProtKB/TrEMBL
  A6HPJ3_RAT UniProtKB/TrEMBL
  A6HPJ4_RAT UniProtKB/TrEMBL
  A6HPJ7_RAT UniProtKB/TrEMBL
  A6HPJ8_RAT UniProtKB/TrEMBL
  CAN3_RAT UniProtKB/Swiss-Prot
  F1LSQ2 ENTREZGENE, UniProtKB/TrEMBL
  O08702 ENTREZGENE, UniProtKB/TrEMBL
  O70376_RAT UniProtKB/TrEMBL
  O70482 ENTREZGENE, UniProtKB/TrEMBL
  P16259 ENTREZGENE
  Q9QZF9 ENTREZGENE, UniProtKB/TrEMBL


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