Capn13 (calpain 13) - Rat Genome Database

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Gene: Capn13 (calpain 13) Rattus norvegicus
Analyze
Symbol: Capn13
Name: calpain 13
RGD ID: 1562682
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); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-activated neutral proteinase 13; calpain-13; CANP 13; MGC109045
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8627,823,664 - 27,918,676 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl627,823,517 - 27,918,665 (+)EnsemblGRCr8
mRatBN7.2622,071,845 - 22,166,864 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl622,071,845 - 22,166,850 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx622,410,052 - 22,498,364 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0622,725,918 - 22,814,231 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0622,205,889 - 22,300,958 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0624,579,590 - 24,676,536 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl624,579,622 - 24,676,524 (-)Ensemblrn6Rnor6.0
Rnor_5.0634,429,074 - 34,525,225 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4622,129,421 - 22,224,086 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera621,618,581 - 21,707,279 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
proteolysis  (IBA,IEA)

Cellular Component
cytoplasm  (IBA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334  


Genomics

Comparative Map Data
Capn13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8627,823,664 - 27,918,676 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl627,823,517 - 27,918,665 (+)EnsemblGRCr8
mRatBN7.2622,071,845 - 22,166,864 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl622,071,845 - 22,166,850 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx622,410,052 - 22,498,364 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0622,725,918 - 22,814,231 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0622,205,889 - 22,300,958 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0624,579,590 - 24,676,536 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl624,579,622 - 24,676,524 (-)Ensemblrn6Rnor6.0
Rnor_5.0634,429,074 - 34,525,225 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4622,129,421 - 22,224,086 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera621,618,581 - 21,707,279 (+)NCBICelera
Cytogenetic Map6q14NCBI
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 (-)Ensemblhg38GRCh38
GRCh37230,945,637 - 31,030,312 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36230,799,141 - 30,883,815 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm381773,306,456 - 73,399,381 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1773,306,464 - 73,400,866 (-)Ensemblmm10GRCm38
MGSCv371773,655,804 - 73,748,636 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361773,211,346 - 73,304,178 (-)NCBIMGSCv36mm8
Celera1777,591,180 - 77,684,049 (-)NCBICelera
Cytogenetic Map17E2NCBI
cM Map1744.84NCBI
Capn13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546912,497,922 - 12,552,125 (-)Ensembl
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1724,179,233 - 24,257,549 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01724,948,327 - 25,026,735 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473812,548,357 - 12,655,347 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Capn13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1719,844,063 - 19,916,586 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Capn13
371 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:279
Count of miRNA genes:186
Interacting mature miRNAs:211
Transcripts:ENSRNOT00000047853
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)62328466429732046Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)62228825732981219Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 33 88 51 53 22 54 22 6 232 115 9 64 71 71 31 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000047853   ⟹   ENSRNOP00000039021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl627,823,549 - 27,918,665 (+)Ensembl
mRatBN7.2 Ensembl622,071,845 - 22,166,850 (+)Ensembl
Rnor_6.0 Ensembl624,579,622 - 24,676,524 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111503   ⟹   ENSRNOP00000077390
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl627,823,549 - 27,918,525 (+)Ensembl
mRatBN7.2 Ensembl622,071,845 - 22,155,553 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000128507   ⟹   ENSRNOP00000108062
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl627,823,549 - 27,918,662 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000160370   ⟹   ENSRNOP00000105700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl627,823,517 - 27,918,664 (+)Ensembl
RefSeq Acc Id: NM_001025133   ⟹   NP_001020304
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8627,823,664 - 27,918,676 (+)NCBI
mRatBN7.2622,071,845 - 22,166,864 (+)NCBI
Rnor_6.0624,579,590 - 24,676,418 (-)NCBI
Rnor_5.0634,429,074 - 34,525,225 (-)NCBI
RGSC_v3.4622,129,421 - 22,224,086 (+)RGD
Celera621,618,581 - 21,707,279 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001020304 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91250 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000039021
  ENSRNOP00000039021.3
GenBank Protein Q5BK10 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020304   ⟸   NM_001025133
- UniProtKB: Q5BK10 (UniProtKB/Swiss-Prot),   A0A8I5Y693 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000039021   ⟸   ENSRNOT00000047853
Ensembl Acc Id: ENSRNOP00000077390   ⟸   ENSRNOT00000111503
Ensembl Acc Id: ENSRNOP00000105700   ⟸   ENSRNOT00000160370
Ensembl Acc Id: ENSRNOP00000108062   ⟸   ENSRNOT00000128507
Protein Domains
Calpain catalytic   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BK10-F1-model_v2 AlphaFold Q5BK10 1-668 view protein structure

Transcriptome

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

Promoters
RGD ID:13694423
Promoter ID:EPDNEW_R4948
Type:multiple initiation site
Name:Capn13_1
Description:calpain 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0624,676,533 - 24,676,593EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562682 AgrOrtholog
BioCyc Gene G2FUF-38420 BioCyc
Ensembl Genes ENSRNOG00000032375 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000047853 ENTREZGENE
  ENSRNOT00000047853.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.380 UniProtKB/Swiss-Prot
  Cysteine proteinases UniProtKB/Swiss-Prot
  EF-hand UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7368359 IMAGE-MGC_LOAD
InterPro Calpain_cysteine_protease UniProtKB/Swiss-Prot
  Calpain_domain_III UniProtKB/Swiss-Prot
  Calpain_III UniProtKB/Swiss-Prot
  Calpain_III_sf UniProtKB/Swiss-Prot
  CAPN3/13-like_C_EFh 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 rno:362701 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109045 IMAGE-MGC_LOAD
NCBI Gene 362701 ENTREZGENE
PANTHER CALPAIN UniProtKB/Swiss-Prot
  PTHR10183:SF333 UniProtKB/Swiss-Prot
Pfam Calpain_III UniProtKB/Swiss-Prot
  CAPN13-like_C_EFh 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
RatGTEx ENSRNOG00000032375 RatGTEx
SMART calpain_III UniProtKB/Swiss-Prot
  CysPc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
  SSF49758 UniProtKB/Swiss-Prot
  SSF54001 UniProtKB/Swiss-Prot
UniProt A0A8I5Y693 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LSG7_RAT UniProtKB/TrEMBL
  A0ABK0LV38_RAT UniProtKB/TrEMBL
  CAN13_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-02-09 Capn13  calpain 13      Symbol and Name status set to provisional 70820 PROVISIONAL