Capn10 (calpain 10) - Rat Genome Database
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Gene: Capn10 (calpain 10) Rattus norvegicus
Analyze
Symbol: Capn10
Name: calpain 10
RGD ID: 69354
Description: Exhibits SNARE binding activity; calcium-dependent cysteine-type endopeptidase activity; and cytoskeletal protein binding activity. Involved in several processes, including actin cytoskeleton reorganization; autophagy of mitochondrion; and response to glucose. Localizes to several cellular components, including cell cortex; cytosol; and mitochondrion. Used to study type 2 diabetes mellitus. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in obesity; pancreatic cancer; polycystic ovary syndrome; and type 2 diabetes mellitus. Orthologous to human CAPN10 (calpain 10); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calcium-activated neutral proteinase 10; calpain-10; CANP 10; MGC93346
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2993,498,132 - 93,510,494 (+)NCBI
Rnor_6.0 Ensembl9100,104,000 - 100,112,832 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09100,104,000 - 100,112,833 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0999,767,655 - 99,776,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera991,034,781 - 91,046,660 (+)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
1. Arrington DD, etal., Am J Physiol Cell Physiol. 2006 Dec;291(6):C1159-71. Epub 2006 Jun 21.
2. Baier LJ, etal., J Clin Invest. 2000 Oct;106(7):R69-73.
3. Covington MD and Schnellmann RG, Kidney Int. 2012 Feb;81(4):391-400. doi: 10.1038/ki.2011.356. Epub 2011 Oct 19.
4. Covington MD, etal., Am J Physiol Renal Physiol. 2009 Mar;296(3):F478-86. Epub 2009 Jan 14.
5. Cox NJ Hum Mol Genet 2001 Oct 1;10(20):2301-5.
6. Demirci H, etal., Genet Test. 2008 Jun;12(2):305-9. doi: 10.1089/gte.2007.0118.
7. Fong PY, etal., J Gastrointest Cancer. 2010 Feb 23.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Kang ES, etal., Diabetes Res Clin Pract. 2006 Sep;73(3):268-75. Epub 2006 Mar 20.
11. Kang ES, etal., J Hum Genet. 2006;51(7):629-33. Epub 2006 May 24.
12. Ling C, etal., PLoS One. 2009 Aug 18;4(8):e6558.
13. Ma H, etal., J Biol Chem 2001 Jul 27;276(30):28525-31.
14. Marshall C, etal., Mol Endocrinol. 2005 Jan;19(1):213-24. Epub 2004 Oct 7.
15. Muramatsu Y, etal., IUBMB Life 2003 Sep;55(9):533-7.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline
18. Pihlajamaki J, etal., Diabetologia. 2006 Jul;49(7):1560-6. Epub 2006 May 12.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Sato Y, etal., Biol Pharm Bull. 2003 Dec;26(12):1765-8.
23. Smith MA, etal., Arch Biochem Biophys. 2012 Jul 15;523(2):161-8. doi: 10.1016/j.abb.2012.04.020. Epub 2012 May 1.
24. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Turner MD, etal., Biochem Biophys Res Commun. 2007 Jan 19;352(3):650-5. Epub 2006 Nov 29.
26. Vollmert C, etal., Am J Physiol Endocrinol Metab. 2007 Mar;292(3):E836-44. Epub 2006 Nov 14.
27. Wu SH, etal., Prostaglandins Leukot Essent Fatty Acids. 2005 Aug;73(2):127-37.
28. Zhou X, etal., Clin Chim Acta. 2010 Aug 5;411(15-16):1126-31. doi: 10.1016/j.cca.2010.04.012. Epub 2010 Apr 18.
Additional References at PubMed
PMID:12477932   PMID:12974673   PMID:15044459   PMID:17572128   PMID:18054326  


Genomics

Comparative Map Data
Capn10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2993,498,132 - 93,510,494 (+)NCBI
Rnor_6.0 Ensembl9100,104,000 - 100,112,832 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09100,104,000 - 100,112,833 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0999,767,655 - 99,776,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera991,034,781 - 91,046,660 (+)NCBICelera
Cytogenetic Map9q36NCBI
CAPN10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2240,586,734 - 240,617,705 (+)EnsemblGRCh38hg38GRCh38
GRCh382240,586,734 - 240,599,104 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,526,151 - 241,538,521 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh372241,526,133 - 241,538,526 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362241,174,818 - 241,205,795 (+)NCBINCBI36hg18NCBI36
Build 342241,246,141 - 241,277,112NCBI
Celera2235,198,477 - 235,210,856 (+)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2233,282,748 - 233,295,178 (+)NCBIHuRef
CHM1_12241,532,185 - 241,544,581 (+)NCBICHM1_1
Capn10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39192,862,130 - 92,875,670 (+)NCBIGRCm39mm39
GRCm38192,934,408 - 92,947,948 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl192,934,376 - 92,947,941 (+)EnsemblGRCm38mm10GRCm38
MGSCv37194,830,985 - 94,844,525 (+)NCBIGRCm37mm9NCBIm37
MGSCv36194,764,814 - 94,778,354 (+)NCBImm8
Celera195,879,004 - 95,892,543 (+)NCBICelera
Cytogenetic Map1DNCBI
Capn10
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955542874,083 - 885,084 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955542874,083 - 885,085 (-)NCBIChiLan1.0ChiLan1.0
CAPN10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B246,645,632 - 246,658,490 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B246,645,630 - 246,679,169 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B127,838,477 - 127,851,334 (+)NCBIMhudiblu_PPA_v0panPan3
CAPN10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2550,555,425 - 50,566,135 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12550,555,402 - 50,566,132 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Capn10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367451,029,514 - 1,039,524 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN10
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15139,557,666 - 139,570,181 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115139,557,643 - 139,568,764 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CAPN10
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110126,613,722 - 126,626,388 (+)NCBI
Capn10
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248474,911,052 - 4,922,549 (+)NCBI

Position Markers
AI430010  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09100,112,413 - 100,112,576NCBIRnor6.0
Rnor_5.0999,776,068 - 99,776,231UniSTSRnor5.0
Celera991,046,240 - 91,046,403UniSTS
Cytogenetic Map9q36UniSTS
RH137033  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09100,112,563 - 100,112,755NCBIRnor6.0
Rnor_5.0999,776,218 - 99,776,410UniSTSRnor5.0
Celera991,046,390 - 91,046,582UniSTS
RH 3.4 Map9796.7UniSTS
Cytogenetic Map9q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)999041068107878528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:305
Count of miRNA genes:201
Interacting mature miRNAs:235
Transcripts:ENSRNOT00000074160
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 20 6 18 6 74 29 41 11
Low 17 37 35 1 35 8 11 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074160   ⟹   ENSRNOP00000067567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9100,104,000 - 100,112,832 (+)Ensembl
RefSeq Acc Id: NM_031673   ⟹   NP_113861
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,498,496 - 93,510,494 (+)NCBI
Rnor_6.09100,104,000 - 100,112,833 (+)NCBI
Rnor_5.0999,767,655 - 99,776,488 (+)NCBI
Celera991,034,781 - 91,046,660 (+)RGD
Sequence:
RefSeq Acc Id: XM_039084156   ⟹   XP_038940084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2993,498,132 - 93,507,229 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113861   ⟸   NM_031673
- UniProtKB: Q9ES66 (UniProtKB/Swiss-Prot),   Q5U345 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067567   ⟸   ENSRNOT00000074160
RefSeq Acc Id: XP_038940084   ⟸   XM_039084156
- Peptide Label: isoform X1
Protein Domains
Calpain catalytic

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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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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 (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
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 (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 (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 (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:69354 AgrOrtholog
Ensembl Genes ENSRNOG00000045623 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067567 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074160 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123652 IMAGE-MGC_LOAD
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
  CAPN10 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:63834 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93346 IMAGE-MGC_LOAD
NCBI Gene 63834 ENTREZGENE
PANTHER PTHR10183:SF30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Capn10 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CALPAIN_CAT 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
Superfamily-SCOP SSF49758 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC231933
UniProt CAN10_RAT UniProtKB/Swiss-Prot
  M0RD70_RAT UniProtKB/TrEMBL
  Q5U345 ENTREZGENE, UniProtKB/TrEMBL
  Q7TQ41_RAT UniProtKB/TrEMBL
  Q9ES66 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Capn10  calpain 10       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease variant of the human homolog is associated with increased risk of type II diabetes 68750
gene_product member of the calpain family of calcium dependent intracellular nonlysosomal proteases 68750