Capns1 (calpain, small subunit 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Capns1 (calpain, small subunit 1) Rattus norvegicus
Analyze
Symbol: Capns1
Name: calpain, small subunit 1
RGD ID: 2270
Description: Contributes to calcium-dependent cysteine-type endopeptidase activity. Involved in protein catabolic process. Predicted to be located in cytosol and membrane. Predicted to be part of calpain complex. Orthologous to human CAPNS1 (calpain small subunit 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-activated neutral proteinase small subunit; calcium-dependent protease small subunit 1; calpain 4; calpain regulatory subunit; calpain small subunit 1; calpain small subunit 1-like; CANP small subunit; Capn4; CDPS; CSS1; LOC100912380
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8194,572,083 - 94,582,332 (-)NCBIGRCr8
mRatBN7.2185,444,613 - 85,454,861 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl185,444,608 - 85,454,795 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx190,861,573 - 90,871,706 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0199,325,245 - 99,335,358 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0192,619,837 - 92,629,970 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0191,058,528 - 91,064,880 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl188,652,446 - 88,657,845 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl188,652,446 - 88,657,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0192,056,305 - 92,207,135 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,519,568 - 85,525,929 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera179,820,845 - 79,830,375 (-)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-alpha-phellandrene  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxybenzoic acid (3,3,5-trimethylcyclohexyl) ester  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
alpha-phellandrene  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (EXP)
cadmium dichloride  (ISO)
calcium silicate  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
crocidolite asbestos  (ISO)
cyproconazole  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
epoxiconazole  (ISO)
Erionite  (ISO)
fenthion  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
gallic acid  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
inulin  (ISO)
ivermectin  (ISO)
kainic acid  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
methidathion  (ISO)
methimazole  (EXP)
microcystin-LR  (ISO)
Nutlin-3  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
silicon dioxide  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
calpain complex  (IBA,IEA,ISO)
cytoplasm  (IEA,ISO)
cytosol  (IEA,ISO)
membrane  (IEA,ISO)
plasma membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Active recombinant rat calpain II. Bacterially produced large and small subunits associate both in vivo and in vitro. Graham-Siegenthaler K, etal., J Biol Chem 1994 Dec 2;269(48):30457-60.
4. Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. Hanna RA, etal., Nature. 2008 Nov 20;456(7220):409-12. doi: 10.1038/nature07451.
5. Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation. Hosfield CM, etal., EMBO J. 1999 Dec 15;18(24):6880-9.
6. Activation of calpain by Ca2+: roles of the large subunit N-terminal and domain III-IV linker peptides. Hosfield CM, etal., J Mol Biol. 2004 Oct 29;343(4):1049-53.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains. Moldoveanu T, etal., Nature. 2008 Nov 20;456(7220):404-8.
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. ERp57-associated mitochondrial micro-calpain truncates apoptosis-inducing factor. Ozaki T, etal., Biochim Biophys Acta. 2008 Oct;1783(10):1955-63. doi: 10.1016/j.bbamcr.2008.05.011. Epub 2008 May 24.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Primary sequences of rat mu-calpain large and small subunits are, respectively, moderately and highly similar to those of human. Sorimachi H, etal., Biochim Biophys Acta 1996 Nov 11;1309(1-2):37-41.
Additional References at PubMed
PMID:9228945   PMID:10825211   PMID:12477932   PMID:14559243   PMID:14579356   PMID:15489334   PMID:15640140   PMID:16877562   PMID:17646163   PMID:18544539   PMID:19199708   PMID:23376485  
PMID:24297866  


Genomics

Comparative Map Data
Capns1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8194,572,083 - 94,582,332 (-)NCBIGRCr8
mRatBN7.2185,444,613 - 85,454,861 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl185,444,608 - 85,454,795 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx190,861,573 - 90,871,706 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0199,325,245 - 99,335,358 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0192,619,837 - 92,629,970 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0191,058,528 - 91,064,880 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl188,652,446 - 88,657,845 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl188,652,446 - 88,657,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0192,056,305 - 92,207,135 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,519,568 - 85,525,929 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera179,820,845 - 79,830,375 (-)NCBICelera
Cytogenetic Map1q21NCBI
CAPNS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381936,140,066 - 36,150,353 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1936,139,953 - 36,150,353 (+)EnsemblGRCh38hg38GRCh38
GRCh371936,630,968 - 36,641,255 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361941,322,758 - 41,333,095 (+)NCBINCBI36Build 36hg18NCBI36
Build 341941,322,757 - 41,333,094NCBI
Celera1933,345,090 - 33,355,427 (+)NCBICelera
Cytogenetic Map19q13.12NCBI
HuRef1933,136,390 - 33,146,727 (+)NCBIHuRef
CHM1_11936,632,259 - 36,643,261 (+)NCBICHM1_1
T2T-CHM13v2.01938,685,882 - 38,696,171 (+)NCBIT2T-CHM13v2.0
Capns1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39729,886,359 - 29,898,308 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl729,886,361 - 29,898,236 (-)EnsemblGRCm39 Ensembl
GRCm38730,186,934 - 30,198,883 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl730,186,936 - 30,198,811 (-)EnsemblGRCm38mm10GRCm38
MGSCv37730,971,961 - 30,980,067 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36729,895,708 - 29,903,784 (-)NCBIMGSCv36mm8
Celera724,783,745 - 24,791,616 (-)NCBICelera
Cytogenetic Map7B1NCBI
cM Map717.31NCBI
Capns1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554682,447,111 - 2,452,982 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554682,446,631 - 2,454,369 (-)NCBIChiLan1.0ChiLan1.0
CAPNS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22042,142,012 - 42,152,045 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11944,125,513 - 44,135,599 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01933,059,291 - 33,069,311 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11941,806,746 - 41,816,507 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1941,806,746 - 41,816,858 (+)Ensemblpanpan1.1panPan2
CAPNS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11116,549,608 - 116,558,928 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1116,550,000 - 116,558,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1115,955,616 - 115,964,853 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01117,151,011 - 117,160,206 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1117,151,015 - 117,159,238 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11116,720,393 - 116,729,644 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01116,340,642 - 116,349,899 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01117,393,688 - 117,402,927 (-)NCBIUU_Cfam_GSD_1.0
Capns1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934911,381,612 - 11,391,526 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936922151,599 - 164,787 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936922151,791 - 161,655 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPNS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl645,511,295 - 45,518,610 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1645,511,410 - 45,518,610 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2640,913,605 - 40,920,805 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CAPNS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1631,049,509 - 31,061,219 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl631,050,494 - 31,061,421 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660738,849,775 - 8,861,494 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capns1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479410,382,157 - 10,390,768 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Capns1
103 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:81
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000072756, ENSRNOT00000074211
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)185424647100358001Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)183547917128547917Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)15034351099980958Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat

Markers in Region
AI844915  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,563,010 - 85,563,149 (+)MAPPERmRatBN7.2
mRatBN7.2185,563,010 - 85,563,149 (-)MAPPERmRatBN7.2
Rnor_6.0188,766,277 - 88,766,415NCBIRnor6.0
Rnor_6.0190,962,959 - 90,963,097NCBIRnor6.0
Rnor_5.0192,100,141 - 92,100,279UniSTSRnor5.0
Rnor_5.0189,922,295 - 89,922,433UniSTSRnor5.0
RGSC_v3.4185,254,595 - 85,254,733UniSTSRGSC3.4
Celera179,936,856 - 79,936,994UniSTS
Cytogenetic Map1q21UniSTS
AI235173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,511,117 - 85,511,248 (+)MAPPERmRatBN7.2
mRatBN7.2185,511,117 - 85,511,248 (-)MAPPERmRatBN7.2
Rnor_6.0191,014,875 - 91,015,005NCBIRnor6.0
Rnor_6.0188,714,415 - 88,714,545NCBIRnor6.0
Rnor_5.0189,871,821 - 89,871,951UniSTSRnor5.0
Rnor_5.0192,152,057 - 92,152,187UniSTSRnor5.0
RGSC_v3.4185,462,793 - 85,462,923UniSTSRGSC3.4
Celera179,885,563 - 79,885,693UniSTS
RH 3.4 Map1845.1UniSTS
Cytogenetic Map1q21UniSTS
RH127933  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,573,578 - 85,573,760 (+)MAPPERmRatBN7.2
mRatBN7.2185,573,578 - 85,573,760 (-)MAPPERmRatBN7.2
Rnor_6.0190,952,346 - 90,952,527NCBIRnor6.0
Rnor_6.0188,776,848 - 88,777,029NCBIRnor6.0
Rnor_5.0189,932,866 - 89,933,047UniSTSRnor5.0
Rnor_5.0192,089,528 - 92,089,709UniSTSRnor5.0
RGSC_v3.4185,265,165 - 85,265,346UniSTSRGSC3.4
Celera179,947,417 - 79,947,598UniSTS
RH 3.4 Map1850.2UniSTS
Cytogenetic Map1q21UniSTS
RH129537  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,576,227 - 85,576,439 (+)MAPPERmRatBN7.2
mRatBN7.2185,576,227 - 85,576,439 (-)MAPPERmRatBN7.2
Rnor_6.0190,949,667 - 90,949,878NCBIRnor6.0
Rnor_6.0188,779,497 - 88,779,708NCBIRnor6.0
Rnor_5.0189,935,515 - 89,935,726UniSTSRnor5.0
Rnor_5.0192,086,849 - 92,087,060UniSTSRnor5.0
RGSC_v3.4185,267,814 - 85,268,025UniSTSRGSC3.4
Celera179,950,066 - 79,950,277UniSTS
RH 3.4 Map1850.2UniSTS
Cytogenetic Map1q21UniSTS
RH133836  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,532,060 - 85,532,247 (+)MAPPERmRatBN7.2
mRatBN7.2185,532,060 - 85,532,247 (-)MAPPERmRatBN7.2
Rnor_6.0190,993,860 - 90,994,046NCBIRnor6.0
Rnor_6.0188,735,722 - 88,735,908NCBIRnor6.0
Rnor_5.0189,891,740 - 89,891,926UniSTSRnor5.0
Rnor_5.0192,131,042 - 92,131,228UniSTSRnor5.0
RGSC_v3.4185,223,648 - 85,223,834UniSTSRGSC3.4
Celera179,906,578 - 79,906,764UniSTS
RH 3.4 Map1850.0UniSTS
Cytogenetic Map1q21UniSTS
D1Bda12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,484,307 - 85,484,531 (+)MAPPERmRatBN7.2
mRatBN7.2185,484,307 - 85,484,531 (-)MAPPERmRatBN7.2
Rnor_6.0188,687,605 - 88,687,828NCBIRnor6.0
Rnor_6.0191,041,592 - 91,041,815NCBIRnor6.0
Rnor_5.0192,178,774 - 92,178,997UniSTSRnor5.0
Rnor_5.0189,845,011 - 89,845,234UniSTSRnor5.0
RGSC_v3.4185,489,510 - 85,489,733UniSTSRGSC3.4
Celera179,858,747 - 79,858,970UniSTS
Cytogenetic Map1q21UniSTS
AI044262  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,562,964 - 85,563,151 (+)MAPPERmRatBN7.2
mRatBN7.2185,562,964 - 85,563,151 (-)MAPPERmRatBN7.2
Rnor_6.0190,962,957 - 90,963,143NCBIRnor6.0
Rnor_6.0188,766,231 - 88,766,417NCBIRnor6.0
Rnor_5.0189,922,249 - 89,922,435UniSTSRnor5.0
Rnor_5.0192,100,139 - 92,100,325UniSTSRnor5.0
RGSC_v3.4185,254,549 - 85,254,735UniSTSRGSC3.4
Celera179,936,810 - 79,936,996UniSTS
RH 3.4 Map1882.29UniSTS
Cytogenetic Map1q21UniSTS
RH137061  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,477,720 - 85,478,039 (+)MAPPERmRatBN7.2
mRatBN7.2185,477,720 - 85,478,039 (-)MAPPERmRatBN7.2
Rnor_6.0191,048,084 - 91,048,402NCBIRnor6.0
Rnor_6.0188,681,018 - 88,681,336NCBIRnor6.0
Rnor_5.0189,838,424 - 89,838,742UniSTSRnor5.0
Rnor_5.0192,185,266 - 92,185,584UniSTSRnor5.0
RGSC_v3.4185,496,002 - 85,496,320UniSTSRGSC3.4
Celera179,852,160 - 79,852,478UniSTS
RH 3.4 Map1848.3UniSTS
Cytogenetic Map1q21UniSTS
RH139378  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,484,547 - 85,484,619 (+)MAPPERmRatBN7.2
mRatBN7.2185,484,547 - 85,484,619 (-)MAPPERmRatBN7.2
Rnor_6.0191,041,504 - 91,041,575NCBIRnor6.0
Rnor_6.0188,687,845 - 88,687,916NCBIRnor6.0
Rnor_5.0189,845,251 - 89,845,322UniSTSRnor5.0
Rnor_5.0192,178,686 - 92,178,757UniSTSRnor5.0
RGSC_v3.4185,489,422 - 85,489,493UniSTSRGSC3.4
Celera179,858,987 - 79,859,058UniSTS
RH 3.4 Map1847.0UniSTS
Cytogenetic Map1q21UniSTS
UniSTS:235641  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,562,890 - 85,563,026 (+)MAPPERmRatBN7.2
mRatBN7.2185,562,890 - 85,563,026 (-)MAPPERmRatBN7.2
Rnor_6.0188,766,157 - 88,766,292NCBIRnor6.0
Rnor_6.0190,963,082 - 90,963,217NCBIRnor6.0
Rnor_5.0192,100,264 - 92,100,399UniSTSRnor5.0
Rnor_5.0189,922,175 - 89,922,310UniSTSRnor5.0
RGSC_v3.4185,254,475 - 85,254,610UniSTSRGSC3.4
Celera179,936,736 - 79,936,871UniSTS
Cytogenetic Map1q21UniSTS
CLIPR-59__4586  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2185,562,383 - 85,563,184 (+)MAPPERmRatBN7.2
mRatBN7.2185,562,383 - 85,563,184 (-)MAPPERmRatBN7.2
Rnor_6.0188,765,650 - 88,766,450NCBIRnor6.0
Rnor_6.0190,962,924 - 90,963,724NCBIRnor6.0
Rnor_5.0192,100,106 - 92,100,906UniSTSRnor5.0
Rnor_5.0189,921,668 - 89,922,468UniSTSRnor5.0
RGSC_v3.4185,253,968 - 85,254,768UniSTSRGSC3.4
Celera179,936,229 - 79,937,029UniSTS
Cytogenetic Map1q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
12 12 62 68 60 36 12 36 12 116 48 38 20 38 24

Sequence


Ensembl Acc Id: ENSRNOT00000072756   ⟹   ENSRNOP00000067513
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl185,444,614 - 85,454,795 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000074211   ⟹   ENSRNOP00000064489
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl185,444,608 - 85,453,800 (-)Ensembl
Rnor_6.0 Ensembl188,652,446 - 88,657,845 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000081362   ⟹   ENSRNOP00000073819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl185,444,696 - 85,453,811 (-)Ensembl
RefSeq Acc Id: NM_017118   ⟹   NP_058814
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8194,572,083 - 94,582,221 (-)NCBI
mRatBN7.2185,444,613 - 85,454,752 (-)NCBI
Rnor_6.0191,058,528 - 91,064,880 (-)NCBI
Rnor_5.0192,056,305 - 92,207,135 (+)NCBI
RGSC_v3.4185,519,568 - 85,525,929 (+)RGD
Celera179,820,845 - 79,830,375 (-)RGD
Sequence:
RefSeq Acc Id: XR_005500363
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8194,572,083 - 94,582,332 (-)NCBI
mRatBN7.2185,444,613 - 85,454,861 (-)NCBI
RefSeq Acc Id: NP_058814   ⟸   NM_017118
- UniProtKB: P97572 (UniProtKB/Swiss-Prot),   Q4V795 (UniProtKB/Swiss-Prot),   Q64537 (UniProtKB/Swiss-Prot),   A6J9U9 (UniProtKB/TrEMBL),   M0RD20 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000064489   ⟸   ENSRNOT00000074211
Ensembl Acc Id: ENSRNOP00000073819   ⟸   ENSRNOT00000081362
Ensembl Acc Id: ENSRNOP00000067513   ⟸   ENSRNOT00000072756
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64537-F1-model_v2 AlphaFold Q64537 1-270 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:2270 AgrOrtholog
BioCyc Gene G2FUF-60140 BioCyc
Ensembl Genes ENSRNOG00000048194 Ensembl
  ENSRNOG00000067065 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00055033452 UniProtKB/Swiss-Prot
  ENSRNOG00060028834 UniProtKB/Swiss-Prot
  ENSRNOG00065034103 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000072756.2 UniProtKB/TrEMBL
  ENSRNOT00000074211.2 UniProtKB/TrEMBL
  ENSRNOT00000081362.2 UniProtKB/TrEMBL
  ENSRNOT00055057849 UniProtKB/Swiss-Prot
  ENSRNOT00060050154 UniProtKB/Swiss-Prot
  ENSRNOT00065058591 UniProtKB/Swiss-Prot
Gene3D-CATH EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7462537 IMAGE-MGC_LOAD
InterPro 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
KEGG Report rno:29156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:116259 IMAGE-MGC_LOAD
NCBI Gene 29156 ENTREZGENE
PANTHER CALPAIN, SMALL SUBUNIT 1 A-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR46735:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EF-hand_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Capns1 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000048194 RatGTEx
  ENSRNOG00000067065 RatGTEx
  ENSRNOG00055033452 RatGTEx
  ENSRNOG00060028834 RatGTEx
  ENSRNOG00065034103 RatGTEx
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K6H7_RAT UniProtKB/TrEMBL
  A6J9U6_RAT UniProtKB/TrEMBL
  A6J9U9 ENTREZGENE, UniProtKB/TrEMBL
  CPNS1_RAT UniProtKB/Swiss-Prot
  M0R533_RAT UniProtKB/TrEMBL
  M0RD20 ENTREZGENE, UniProtKB/TrEMBL
  P97572 ENTREZGENE
  Q4V795 ENTREZGENE
  Q64537 ENTREZGENE
UniProt Secondary P97572 UniProtKB/Swiss-Prot
  Q4V795 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Capns1  calpain, small subunit 1  LOC100912380  calpain small subunit 1-like  Data merged from RGD:6487412 737654 PROVISIONAL
2012-07-05 LOC100912380  calpain small subunit 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Capns1  calpain, small subunit 1       Symbol and Name status set to approved 70586 APPROVED
2002-02-27 Capns1  calpain, small subunit 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70292 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function calcium-activated protease subunit; works only in conjuction with large subunit 634695
gene_homology 94% identical to human homolog 69793
gene_physical_interaction interacts with large subunit of calpain 634695
gene_protein 21 kDa protein 634695