Capn13 (calpain 13) - Rat Genome Database

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Gene: Capn13 (calpain 13) Mus musculus
Analyze
Symbol: Capn13
Name: calpain 13
RGD ID: 1621953
MGI Page MGI
Description: Predicted to enable calcium-dependent cysteine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be active in cytoplasm. Orthologous to human CAPN13 (calpain 13).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-activated neutral proteinase 13; calpain-13; CANP 13; Gm943
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391773,613,451 - 73,706,376 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1773,613,459 - 73,707,861 (-)EnsemblGRCm39 Ensembl
GRCm381773,306,456 - 73,399,381 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1773,306,464 - 73,400,866 (-)EnsemblGRCm38mm10GRCm38
MGSCv371773,655,804 - 73,748,636 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361773,211,346 - 73,304,178 (-)NCBIMGSCv36mm8
Celera1777,591,180 - 77,684,049 (-)NCBICelera
Cytogenetic Map17E2NCBI
cM Map1744.84NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
proteolysis  (IBA)

Cellular Component
cytoplasm  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:16141072   PMID:16141073   PMID:21677750   PMID:21829440   PMID:21873635  


Genomics

Comparative Map Data
Capn13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391773,613,451 - 73,706,376 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1773,613,459 - 73,707,861 (-)EnsemblGRCm39 Ensembl
GRCm381773,306,456 - 73,399,381 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1773,306,464 - 73,400,866 (-)EnsemblGRCm38mm10GRCm38
MGSCv371773,655,804 - 73,748,636 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361773,211,346 - 73,304,178 (-)NCBIMGSCv36mm8
Celera1777,591,180 - 77,684,049 (-)NCBICelera
Cytogenetic Map17E2NCBI
cM Map1744.84NCBI
CAPN13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38230,722,771 - 30,807,446 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl230,722,771 - 30,820,542 (-)EnsemblGRCh38hg38GRCh38
GRCh37230,945,637 - 31,030,312 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36230,799,141 - 30,883,815 (-)NCBINCBI36Build 36hg18NCBI36
Build 34230,857,290 - 30,941,962NCBI
Celera230,788,751 - 30,873,413 (-)NCBICelera
Cytogenetic Map2p23.1NCBI
HuRef230,683,655 - 30,768,006 (-)NCBIHuRef
CHM1_1230,875,937 - 30,960,642 (-)NCBICHM1_1
T2T-CHM13v2.0230,767,038 - 30,851,702 (-)NCBIT2T-CHM13v2.0
Capn13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8627,823,664 - 27,918,676 (+)NCBIGRCr8
mRatBN7.2622,071,845 - 22,166,864 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl622,071,845 - 22,166,850 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx622,410,052 - 22,498,364 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0622,725,918 - 22,814,231 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0622,205,889 - 22,300,958 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0624,579,590 - 24,676,536 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl624,579,622 - 24,676,524 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0634,429,074 - 34,525,225 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4622,129,421 - 22,224,086 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera621,618,581 - 21,707,279 (+)NCBICelera
Cytogenetic Map6q14NCBI
Capn13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546912,497,922 - 12,552,125 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546912,497,890 - 12,569,453 (-)NCBIChiLan1.0ChiLan1.0
CAPN13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21295,690,838 - 95,775,620 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A95,694,812 - 95,779,594 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A30,735,412 - 30,820,237 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A30,808,764 - 30,893,391 (-)NCBIpanpan1.1PanPan1.1panPan2
CAPN13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11724,384,992 - 24,446,201 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1724,384,978 - 24,463,355 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1724,179,233 - 24,257,549 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01724,948,327 - 25,026,735 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1724,948,313 - 25,026,766 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11724,251,809 - 24,330,112 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01724,313,640 - 24,391,950 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01724,413,445 - 24,491,877 (-)NCBIUU_Cfam_GSD_1.0
Capn13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629268,499,713 - 68,570,204 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364932,283,955 - 2,338,868 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364932,283,955 - 2,338,868 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3108,531,147 - 108,620,616 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13108,530,743 - 108,621,119 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23115,216,150 - 115,260,923 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CAPN13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11476,695,370 - 76,810,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1476,704,809 - 76,793,342 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604535,294,725 - 35,379,807 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capn13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473812,583,329 - 12,638,646 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473812,548,357 - 12,655,347 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Capn13
3576 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:213
Count of miRNA genes:174
Interacting mature miRNAs:195
Transcripts:ENSMUST00000095208
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301338Lmr1_mleishmaniasis resistance 1 (mouse)Not determined171008134086996400Mouse
4142150Stheal11_msoft tissue heal 11 (mouse)Not determined171228621183361768Mouse
4141319Hmtb8_mhemostasis and thrombosis rebleeding time 8 (mouse)Not determined4053444774534623Mouse
15039324Nmrs48_mNAFLD-associated magnetic resonance shift 48 (mouse)174093918774939187Mouse
26884428Cvht3_mcranial vault height 3, 5 week (mouse)174651092682407429Mouse
1357754Ahl3_mage related hearing loss 3 (mouse)Not determined175020395784204103Mouse
4141879Chlq9_mcirculating hormone level QTL 9 (mouse)Not determined175175842585758612Mouse
1357532Bmch7_mbone mechanical trait 7 (mouse)Not determined175175842585758612Mouse
1357447Heal13_mwound healing/regeneration 13 (mouse)Not determined175710765191107803Mouse
4141758Pstc5_mperiosteal circumference 5 (mouse)Not determined175710765191107803Mouse
4141011Bmd26_mbone mineral density 26 (mouse)Not determined175710765191107803Mouse
1300735Pgia20_mproteoglycan induced arthritis 20 (mouse)Not determined175710765191107803Mouse
12910536Nrq8a_mnoise-induced hearing loss resistant QTL 8a (mouse)175710765191107803Mouse
12910537Nrq8_mnoise-induced hearing loss resistant QTL 8 (mouse)175710765191107803Mouse
4142201Obrq15_mobesity resistance QTL 15 (mouse)Not determined5753444780885776Mouse
4142414Pregq4_mpregnancy QTL 4 (mouse)Not determined175753444793507179Mouse
4141040Hmtb9_mhemostasis and thrombosis rebleeding time 9 (mouse)Not determined5758908991589197Mouse
1301107Scc4_mcolon tumor susceptibility 4 (mouse)Not determined176230101095294699Mouse
11528551Sluc32_msusceptibility to lung cancer 32 (mouse)176230101095294699Mouse
1302017Aliq3_macute lung injury QTL 3 (mouse)Not determined176388554895294699Mouse
1301728Ffal1_mfree fatty acid level 1 (mouse)Not determined176521493895294699Mouse
14928308Manh82_mmandible shape 82 (mouse)176631524395294699Mouse
13464254Ifvrq3_minfluenza virus resistance QTL 3 (mouse)176795765583908089Mouse
4142256Nilac12_mnicotine induced locomotor activity 12 (mouse)Not determined176894131995294699Mouse
11039500Ltpr7c_mLeishmania tropica response 7c (mouse)177070119895294699Mouse
11039498Ltpr7b_mLeishmania tropica response 7b (mouse)177070119895294699Mouse
11039499Ltpr7a_mLeishmania tropica response 7a (mouse)177070119895294699Mouse
11039514Ltpr7_mLeishmania tropica response 7 (mouse)177070119895294699Mouse
11565819Ppipq1_mprepulse inhibition percentage QTL 1 (mouse)177105765575377655Mouse
4141391Lfnq6_mlung function QTL 6 (mouse)Not determined7217488874125620Mouse
1357528Nhdlq3_mnon-HDL QTL 3 (mouse)Not determined177339513295294699Mouse
4141195Nilac11_mnicotine induced locomotor activity 11 (mouse)Not determined177339513295294699Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000095208   ⟹   ENSMUSP00000092832
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1773,613,459 - 73,706,291 (-)Ensembl
GRCm38.p6 Ensembl1773,306,464 - 73,399,296 (-)Ensembl
RefSeq Acc Id: ENSMUST00000233432
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1773,651,917 - 73,707,861 (-)Ensembl
GRCm38.p6 Ensembl1773,344,922 - 73,400,866 (-)Ensembl
RefSeq Acc Id: NM_001033444   ⟹   NP_001028616
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391773,613,459 - 73,706,291 (-)NCBI
GRCm381773,306,464 - 73,399,296 (-)NCBI
MGSCv371773,655,804 - 73,748,636 (-)RGD
Celera1777,591,180 - 77,684,049 (-)RGD
cM Map17 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006524535   ⟹   XP_006524598
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391773,638,086 - 73,706,376 (-)NCBI
GRCm381773,331,091 - 73,399,381 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017317548   ⟹   XP_017173037
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391773,613,451 - 73,673,025 (-)NCBI
GRCm381773,306,456 - 73,366,030 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001782085
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391773,631,764 - 73,706,376 (-)NCBI
GRCm381773,324,769 - 73,399,381 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001028616   ⟸   NM_001033444
- UniProtKB: B2RW21 (UniProtKB/Swiss-Prot),   Q3UW68 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006524598   ⟸   XM_006524535
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017173037   ⟸   XM_017317548
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000092832   ⟸   ENSMUST00000095208
Protein Domains
Calpain catalytic   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3UW68-F1-model_v2 AlphaFold Q3UW68 1-665 view protein structure

Promoters
RGD ID:13676750
Promoter ID:EPDNEW_M22524
Type:multiple initiation site
Name:Capn13_1
Description:Mus musculus calpain 13 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381773,399,296 - 73,399,356EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2685789 AgrOrtholog
Ensembl Genes ENSMUSG00000043705 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000095208 ENTREZGENE
  ENSMUST00000095208.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.380 UniProtKB/Swiss-Prot
  Cysteine proteinases UniProtKB/Swiss-Prot
  EF-hand UniProtKB/Swiss-Prot
InterPro Calpain_cysteine_protease UniProtKB/Swiss-Prot
  Calpain_domain_III UniProtKB/Swiss-Prot
  Calpain_III_sf UniProtKB/Swiss-Prot
  EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot
  Pept_cys_AS UniProtKB/Swiss-Prot
  Peptidase_C2_calpain_cat UniProtKB/Swiss-Prot
KEGG Report mmu:381122 UniProtKB/Swiss-Prot
MGD MGI:2685789 ENTREZGENE
NCBI Gene 381122 ENTREZGENE
PANTHER CALPAIN UniProtKB/Swiss-Prot
  PTHR10183:SF333 UniProtKB/Swiss-Prot
Pfam Calpain_III UniProtKB/Swiss-Prot
  Peptidase_C2 UniProtKB/Swiss-Prot
PhenoGen Capn13 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot
PROSITE CALPAIN_CAT UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
  THIOL_PROTEASE_CYS UniProtKB/Swiss-Prot
SMART CysPc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
  SSF49758 UniProtKB/Swiss-Prot
  SSF54001 UniProtKB/Swiss-Prot
UniProt B2RW21 ENTREZGENE
  CAN13_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2RW21 UniProtKB/Swiss-Prot