Capn12 (calpain 12) - Rat Genome Database

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Gene: Capn12 (calpain 12) Rattus norvegicus
Analyze
Symbol: Capn12
Name: calpain 12
RGD ID: 1307341
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 CAPN12 (calpain 12); INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: calpain-12; LOC308476
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
GRCr8193,298,571 - 93,311,220 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl193,298,571 - 93,310,630 (+)EnsemblGRCr8
mRatBN7.2184,171,059 - 84,183,161 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl184,171,059 - 84,183,119 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx189,580,975 - 89,593,038 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0198,040,078 - 98,052,143 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0191,336,837 - 91,348,901 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0187,066,289 - 87,078,348 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl187,066,289 - 87,078,348 (+)Ensemblrn6Rnor6.0
Rnor_5.0188,246,907 - 88,258,966 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4183,989,000 - 84,001,059 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera178,561,187 - 78,573,226 (+)NCBICelera
RGSC_v3.1184,066,985 - 84,078,502 (+)NCBI
Cytogenetic Map1q21NCBI
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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

Genomics

Comparative Map Data
Capn12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8193,298,571 - 93,311,220 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl193,298,571 - 93,310,630 (+)EnsemblGRCr8
mRatBN7.2184,171,059 - 84,183,161 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl184,171,059 - 84,183,119 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx189,580,975 - 89,593,038 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0198,040,078 - 98,052,143 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0191,336,837 - 91,348,901 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0187,066,289 - 87,078,348 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl187,066,289 - 87,078,348 (+)Ensemblrn6Rnor6.0
Rnor_5.0188,246,907 - 88,258,966 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4183,989,000 - 84,001,059 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera178,561,187 - 78,573,226 (+)NCBICelera
RGSC_v3.1184,066,985 - 84,078,502 (+)NCBI
Cytogenetic Map1q21NCBI
CAPN12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381938,730,192 - 38,744,693 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1938,730,187 - 38,769,904 (-)Ensemblhg38GRCh38
GRCh371939,220,832 - 39,235,114 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361943,912,672 - 43,926,954 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341943,912,671 - 43,926,954NCBI
Celera1936,022,825 - 36,037,032 (-)NCBICelera
Cytogenetic Map19q13.2NCBI
HuRef1935,667,615 - 35,682,075 (-)NCBIHuRef
CHM1_11939,221,640 - 39,235,595 (-)NCBICHM1_1
T2T-CHM13v2.01941,534,246 - 41,548,645 (-)NCBIT2T-CHM13v2.0
Capn12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,580,890 - 28,593,010 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl728,580,847 - 28,592,988 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38728,881,465 - 28,893,585 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,881,422 - 28,893,563 (+)Ensemblmm10GRCm38
MGSCv37729,666,675 - 29,678,604 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36728,590,417 - 28,602,345 (+)NCBIMGSCv36mm8
Celera723,443,096 - 23,455,025 (+)NCBICelera
Cytogenetic Map7B1NCBI
cM Map716.94NCBI
Capn12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955468761,015 - 770,327 (+)Ensembl
ChiLan1.0NW_004955468761,015 - 771,387 (+)NCBIChiLan1.0ChiLan1.0
CAPN12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22045,022,279 - 45,036,564 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11946,892,628 - 46,907,061 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01935,824,858 - 35,839,633 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11944,396,099 - 44,409,441 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1944,394,323 - 44,409,441 (-)EnsemblpanPan2panpan1.1
CAPN12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11114,342,210 - 114,347,873 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1114,342,521 - 114,354,482 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1113,747,505 - 113,759,624 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01114,944,822 - 114,956,873 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1114,942,987 - 114,956,640 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11114,518,101 - 114,530,073 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01114,135,462 - 114,147,615 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01115,174,114 - 115,186,160 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Capn12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934913,237,769 - 13,261,377 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368011,403,256 - 1,412,570 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049368011,402,813 - 1,426,733 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl647,565,440 - 47,578,994 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1647,565,917 - 47,579,278 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2643,126,499 - 43,139,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CAPN12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1633,372,942 - 33,403,800 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl633,373,372 - 33,385,758 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607311,323,650 - 11,370,402 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capn12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479412,113,970 - 12,124,499 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462479412,114,392 - 12,125,633 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Capn12
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12167,108,955 - 167,120,174 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Capn12
85 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:59
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000027645
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)18126986099645535Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat

Markers in Region
RH130124  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2184,182,829 - 84,183,027 (+)MAPPERmRatBN7.2
Rnor_6.0187,078,059 - 87,078,256NCBIRnor6.0
Rnor_5.0188,258,677 - 88,258,874UniSTSRnor5.0
RGSC_v3.4184,000,770 - 84,000,967UniSTSRGSC3.4
Celera178,572,937 - 78,573,134UniSTS
RH 3.4 Map1829.8UniSTS
Cytogenetic Map1q22UniSTS
Cytogenetic Map1q21UniSTS


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 67 157 91 90 59 90 59 6 354 190 11 136 81 91 31 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000027645   ⟹   ENSRNOP00000027645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl193,298,571 - 93,310,630 (+)Ensembl
mRatBN7.2 Ensembl184,171,059 - 84,183,119 (+)Ensembl
Rnor_6.0 Ensembl187,066,289 - 87,078,348 (+)Ensembl
RefSeq Acc Id: NM_001110808   ⟹   NP_001104278
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8193,298,571 - 93,310,630 (+)NCBI
mRatBN7.2184,171,059 - 84,183,119 (+)NCBI
Rnor_6.0187,066,289 - 87,078,348 (+)NCBI
Rnor_5.0188,246,907 - 88,258,966 (+)NCBI
RGSC_v3.4183,989,000 - 84,001,059 (+)RGD
Celera178,561,187 - 78,573,226 (+)RGD
Sequence:
RefSeq Acc Id: XM_039111580   ⟹   XP_038967508
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8193,298,675 - 93,311,220 (+)NCBI
mRatBN7.2184,171,134 - 84,183,161 (+)NCBI
RefSeq Acc Id: XM_039111581   ⟹   XP_038967509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8193,298,675 - 93,309,709 (+)NCBI
mRatBN7.2184,171,134 - 84,182,198 (+)NCBI
RefSeq Acc Id: XR_005505354
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8193,298,675 - 93,309,826 (+)NCBI
mRatBN7.2184,171,134 - 84,182,315 (+)NCBI
RefSeq Acc Id: NP_001104278   ⟸   NM_001110808
- UniProtKB: D3ZJZ8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027645   ⟸   ENSRNOT00000027645
RefSeq Acc Id: XP_038967508   ⟸   XM_039111580
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967509   ⟸   XM_039111581
- Peptide Label: isoform X2
Protein Domains
Calpain catalytic   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJZ8-F1-model_v2 AlphaFold D3ZJZ8 1-719 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:1307341 AgrOrtholog
BioCyc Gene G2FUF-60207 BioCyc
Ensembl Genes ENSRNOG00000020389 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027645 ENTREZGENE
  ENSRNOT00000027645.6 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.380 UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro C2_III UniProtKB/TrEMBL
  Calpain_cysteine_protease UniProtKB/TrEMBL
  Calpain_domain_III UniProtKB/TrEMBL
  Calpain_III UniProtKB/TrEMBL
  Calpain_III_sf UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Pept_cys_AS UniProtKB/TrEMBL
  Peptidase_C2_calpain_cat UniProtKB/TrEMBL
KEGG Report rno:308476 UniProtKB/TrEMBL
NCBI Gene 308476 ENTREZGENE
PANTHER CALPAIN UniProtKB/TrEMBL
  PTHR10183:SF280 UniProtKB/TrEMBL
Pfam Calpain_III UniProtKB/TrEMBL
  Peptidase_C2 UniProtKB/TrEMBL
PhenoGen Capn12 PhenoGen
PRINTS CALPAIN UniProtKB/TrEMBL
PROSITE CALPAIN_CAT UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
  THIOL_PROTEASE_CYS UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020389 RatGTEx
SMART calpain_III UniProtKB/TrEMBL
  CysPc UniProtKB/TrEMBL
Superfamily-SCOP Peptidase_C2 UniProtKB/TrEMBL
  SSF47473 UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt D3ZJZ8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Capn12  calpain 12   Capn12_predicted  calpain 12 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Capn12_predicted  calpain 12 (predicted)      Symbol and Name status set to approved 70820 APPROVED