Capn11 (calpain 11) - Rat Genome Database

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Gene: Capn11 (calpain 11) Rattus norvegicus
Analyze
Symbol: Capn11
Name: calpain 11
RGD ID: 1302946
Description: Predicted to enable calcium-dependent cysteine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in acrosomal vesicle. Predicted to be active in cytoplasm. Orthologous to human CAPN11 (calpain 11); INTERACTS WITH bisphenol A; 2,3,7,8-tetrachlorodibenzodioxine (ortholog); 5-aza-2'-deoxycytidine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: calcium-activated neutral proteinase 11; CANP 11
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
mRatBN7.2915,344,059 - 15,365,604 (+)NCBI
Rnor_6.0 Ensembl917,728,816 - 17,750,363 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0917,728,845 - 17,750,357 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0916,617,234 - 16,638,763 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,944,080 - 10,965,592 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,946,925 - 10,962,499 (+)NCBI
Celera913,088,339 - 13,109,769 (+)NCBICelera
Cytogenetic Map9q12NCBI
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,IEA)

Cellular Component
acrosomal vesicle  (IEA,ISO)
cytoplasm  (IBA)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16541461  


Genomics

Comparative Map Data
Capn11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2915,344,059 - 15,365,604 (+)NCBI
Rnor_6.0 Ensembl917,728,816 - 17,750,363 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0917,728,845 - 17,750,357 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0916,617,234 - 16,638,763 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,944,080 - 10,965,592 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,946,925 - 10,962,499 (+)NCBI
Celera913,088,339 - 13,109,769 (+)NCBICelera
Cytogenetic Map9q12NCBI
CAPN11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl644,158,811 - 44,184,401 (+)EnsemblGRCh38hg38GRCh38
GRCh38644,158,811 - 44,184,401 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37644,126,557 - 44,152,138 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36644,234,526 - 44,260,117 (+)NCBINCBI36hg18NCBI36
Build 34644,234,525 - 44,260,117NCBI
Celera645,679,690 - 45,705,285 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef643,847,872 - 43,873,397 (+)NCBIHuRef
CHM1_1644,130,722 - 44,155,885 (+)NCBICHM1_1
Capn11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391745,941,117 - 45,970,400 (-)NCBIGRCm39mm39
GRCm39 Ensembl1745,941,130 - 45,970,251 (-)Ensembl
GRCm381745,630,191 - 45,659,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1745,630,204 - 45,659,325 (-)EnsemblGRCm38mm10GRCm38
MGSCv371745,767,153 - 45,796,258 (-)NCBIGRCm37mm9NCBIm37
MGSCv361745,093,785 - 45,122,890 (-)NCBImm8
Celera1749,065,616 - 49,089,535 (-)NCBICelera
Cytogenetic Map17CNCBI
Capn11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554379,791,021 - 9,804,769 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554379,791,021 - 9,804,769 (+)NCBIChiLan1.0ChiLan1.0
CAPN11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1645,040,057 - 45,064,765 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl645,040,057 - 45,064,765 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0643,753,201 - 43,780,465 (+)NCBIMhudiblu_PPA_v0panPan3
CAPN11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11212,580,952 - 12,604,973 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1212,580,252 - 12,598,633 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1212,607,222 - 12,625,764 (+)NCBI
ROS_Cfam_1.01213,063,224 - 13,081,793 (+)NCBI
UMICH_Zoey_3.11212,588,865 - 12,607,347 (+)NCBI
UNSW_CanFamBas_1.01212,676,546 - 12,695,304 (+)NCBI
UU_Cfam_GSD_1.01212,770,497 - 12,789,068 (+)NCBI
Capn11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494648,052,339 - 48,071,166 (+)NCBI
SpeTri2.0NW_00493647615,889,330 - 15,901,169 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl739,168,677 - 39,191,396 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1739,168,991 - 39,191,934 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2744,986,150 - 45,010,543 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CAPN11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11727,980,271 - 28,006,358 (-)NCBI
ChlSab1.1 Ensembl1727,980,140 - 27,997,256 (-)Ensembl
Vero_WHO_p1.0NW_02366604444,214,982 - 44,241,532 (+)NCBI
Capn11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475415,673,042 - 15,682,891 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:306
Count of miRNA genes:161
Interacting mature miRNAs:175
Transcripts:ENSRNOT00000065754, ENSRNOT00000067104
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 7
Low 2
Below cutoff 1 2 10 7 2 7 2 3 18 8 19 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065754   ⟹   ENSRNOP00000059934
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl917,728,816 - 17,750,363 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067104   ⟹   ENSRNOP00000061253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl917,734,345 - 17,749,942 (+)Ensembl
RefSeq Acc Id: NM_001002806   ⟹   NP_001002806
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2915,344,089 - 15,365,604 (+)NCBI
Rnor_6.0917,728,845 - 17,750,357 (+)NCBI
Rnor_5.0916,617,234 - 16,638,763 (+)NCBI
RGSC_v3.4910,944,080 - 10,965,592 (+)RGD
Celera913,088,339 - 13,109,769 (+)RGD
Sequence:
RefSeq Acc Id: XM_039084029   ⟹   XP_038939957
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2915,344,059 - 15,365,500 (+)NCBI
RefSeq Acc Id: XM_039084030   ⟹   XP_038939958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2915,344,059 - 15,364,192 (+)NCBI
RefSeq Acc Id: XM_039084031   ⟹   XP_038939959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2915,344,059 - 15,365,500 (+)NCBI
RefSeq Acc Id: XM_039084033   ⟹   XP_038939961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2915,344,059 - 15,364,375 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001002806   ⟸   NM_001002806
- UniProtKB: Q4V8Q1 (UniProtKB/Swiss-Prot),   D3ZXF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061253   ⟸   ENSRNOT00000067104
RefSeq Acc Id: ENSRNOP00000059934   ⟸   ENSRNOT00000065754
RefSeq Acc Id: XP_038939957   ⟸   XM_039084029
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939959   ⟸   XM_039084031
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939961   ⟸   XM_039084033
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038939958   ⟸   XM_039084030
- Peptide Label: isoform X2
Protein Domains
Calpain catalytic   EF-hand

Transcriptome

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

Promoters
RGD ID:13696538
Promoter ID:EPDNEW_R7063
Type:multiple initiation site
Name:Capn11_1
Description:calpain 11
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_6.0917,728,843 - 17,728,903EPDNEW

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)
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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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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/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:1302946 AgrOrtholog
Ensembl Genes ENSRNOG00000026025 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059934 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000061253 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065754 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000067104 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7457866 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
  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
  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:408218 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:114218 IMAGE-MGC_LOAD
NCBI Gene 408218 ENTREZGENE
Pfam Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Capn11 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CALPAIN_CAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 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
  EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49758 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CAN11_RAT UniProtKB/Swiss-Prot
  D3ZXF4 ENTREZGENE, UniProtKB/TrEMBL
  F1M7U2_RAT UniProtKB/TrEMBL
  Q4V8Q1 ENTREZGENE
UniProt Secondary Q6IE72 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-02-14 Capn11  calpain 11      Symbol and Name status set to provisional 70820 PROVISIONAL