Capn9 (calpain 9) - Rat Genome Database

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Gene: Capn9 (calpain 9) Rattus norvegicus
Analyze
Symbol: Capn9
Name: calpain 9
RGD ID: 70965
Description: Predicted to enable calcium-dependent cysteine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in stomach cancer. Orthologous to human CAPN9 (calpain 9); INTERACTS WITH 1-naphthyl isothiocyanate; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: calpain 9 (nCL-4); calpain-9; digestive tract-specific calpain; Ncl-4; new calpain 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,446,847 - 69,483,810 (+)NCBIGRCr8
mRatBN7.21952,549,448 - 52,586,413 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,549,448 - 52,586,413 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,334,438 - 59,371,384 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,186,063 - 60,223,037 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,260,893 - 62,297,832 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,341,938 - 57,378,901 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,341,938 - 57,378,901 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01968,047,157 - 68,084,264 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,759,009 - 54,796,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11954,763,943 - 54,801,111 (+)NCBI
Celera1951,919,286 - 51,955,889 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. Molecular cloning and characterization of a novel tissue-specific calpain predominantly expressed in the digestive tract. Lee HJ, etal., Biol Chem 1998 Feb;379(2):175-83.
4. Down-regulation of calpain 9 is linked to hypertensive heart and kidney disease. Markmann A, etal., Cell Physiol Biochem. 2005;15(1-4):109-16. doi: 10.1159/000083643.
5. Gene Data Set MGD Curation, June 12, 2002
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. GOA pipeline RGD automated data pipeline
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Isolation of two novel genes, down-regulated in gastric cancer. Yoshikawa Y, etal., Jpn J Cancer Res 2000 May;91(5):459-63.

Genomics

Comparative Map Data
Capn9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,446,847 - 69,483,810 (+)NCBIGRCr8
mRatBN7.21952,549,448 - 52,586,413 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,549,448 - 52,586,413 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,334,438 - 59,371,384 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,186,063 - 60,223,037 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,260,893 - 62,297,832 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,341,938 - 57,378,901 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,341,938 - 57,378,901 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01968,047,157 - 68,084,264 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,759,009 - 54,796,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11954,763,943 - 54,801,111 (+)NCBI
Celera1951,919,286 - 51,955,889 (+)NCBICelera
Cytogenetic Map19q12NCBI
CAPN9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381230,747,388 - 230,801,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1230,747,384 - 230,802,003 (+)EnsemblGRCh38hg38GRCh38
GRCh371230,883,134 - 230,937,735 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361228,949,753 - 229,004,372 (+)NCBINCBI36Build 36hg18NCBI36
Build 341227,189,864 - 227,244,253NCBI
Celera1204,149,151 - 204,203,730 (+)NCBICelera
Cytogenetic Map1q42.2NCBI
HuRef1201,367,929 - 201,422,446 (+)NCBIHuRef
CHM1_11232,156,149 - 232,210,762 (+)NCBICHM1_1
T2T-CHM13v2.01230,127,941 - 230,182,452 (+)NCBIT2T-CHM13v2.0
Capn9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,301,361 - 125,345,470 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8125,302,850 - 125,345,470 (+)EnsemblGRCm39 Ensembl
GRCm388124,576,062 - 124,618,731 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,576,111 - 124,618,731 (+)EnsemblGRCm38mm10GRCm38
MGSCv378127,100,011 - 127,142,631 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368127,462,201 - 127,504,812 (+)NCBIMGSCv36mm8
Celera8128,879,934 - 128,910,507 (+)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.81NCBI
Capn9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554927,809,188 - 7,845,090 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554927,809,188 - 7,845,090 (-)NCBIChiLan1.0ChiLan1.0
CAPN9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,411,108 - 18,459,432 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,602,251 - 18,651,772 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01206,297,088 - 206,347,427 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11211,324,405 - 211,378,944 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1211,324,405 - 211,378,944 (+)Ensemblpanpan1.1panPan2
CAPN9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.148,613,222 - 8,653,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl48,612,682 - 8,653,467 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha48,604,905 - 8,645,249 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.048,637,647 - 8,677,873 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl48,637,107 - 8,678,521 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.148,641,831 - 8,682,029 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.048,763,717 - 8,803,940 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.048,993,883 - 9,034,136 (-)NCBIUU_Cfam_GSD_1.0
Capn9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,506,573 - 43,534,017 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648419,671,964 - 19,699,161 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648419,671,799 - 19,699,161 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,582,046 - 59,623,376 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11459,581,999 - 59,623,553 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21464,246,812 - 64,288,645 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CAPN9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12568,018,785 - 68,072,299 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2568,019,375 - 68,072,123 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605569,925,003 - 69,973,406 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capn9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477518,790,527 - 18,826,830 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477518,792,599 - 18,827,082 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Capn9
349 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:79
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000025357
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat

Markers in Region
RH137412  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21952,586,202 - 52,586,416 (+)MAPPERmRatBN7.2
Rnor_6.01957,378,691 - 57,378,904NCBIRnor6.0
Rnor_5.01968,084,054 - 68,084,267UniSTSRnor5.0
RGSC_v3.41954,796,180 - 54,796,393UniSTSRGSC3.4
RH 3.4 Map19721.8UniSTS
Cytogenetic Map19q12UniSTS


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 nervous system renal system reproductive system respiratory system
High
Medium 2
Low 1 2 2 1 2 1
Below cutoff 7 14 7 10 7 6 6 18 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025357   ⟹   ENSRNOP00000025357
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1952,549,448 - 52,586,413 (+)Ensembl
Rnor_6.0 Ensembl1957,341,938 - 57,378,901 (+)Ensembl
RefSeq Acc Id: NM_001271140   ⟹   NP_001258069
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,446,847 - 69,483,810 (+)NCBI
mRatBN7.21952,549,448 - 52,586,413 (+)NCBI
Rnor_6.01957,341,938 - 57,378,901 (+)NCBI
Rnor_5.01968,047,157 - 68,084,264 (+)NCBI
Celera1951,919,286 - 51,955,889 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001258069 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB69115 (Get FASTA)   NCBI Sequence Viewer  
  EDL96734 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000025357
  ENSRNOP00000025357.7
  ENSRNOP00055028074
GenBank Protein O35920 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001258069   ⟸   NM_001271140
- UniProtKB: F1LR50 (UniProtKB/Swiss-Prot),   O35920 (UniProtKB/Swiss-Prot),   A6KJ12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025357   ⟸   ENSRNOT00000025357
Protein Domains
Calpain catalytic   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35920-F1-model_v2 AlphaFold O35920 1-690 view protein structure

Transcriptome

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

Promoters
RGD ID:13701235
Promoter ID:EPDNEW_R11759
Type:single initiation site
Name:Capn9_1
Description:calpain 9
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_6.01957,341,934 - 57,341,994EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70965 AgrOrtholog
BioCyc Gene G2FUF-5243 BioCyc
Ensembl Genes ENSRNOG00000018480 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055020281 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025357 ENTREZGENE
  ENSRNOT00000025357.8 UniProtKB/Swiss-Prot
  ENSRNOT00055034649 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.380 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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:116694 UniProtKB/Swiss-Prot
NCBI Gene 116694 ENTREZGENE
PANTHER CALPAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CALPAIN-9 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam Calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Capn9 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
RatGTEx ENSRNOG00000018480 RatGTEx
  ENSRNOG00055020281 RatGTEx
SMART calpain_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CysPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Calpain large subunit, middle domain (domain III) UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  SSF49758 UniProtKB/Swiss-Prot
  SSF54001 UniProtKB/Swiss-Prot
UniProt A6KJ12 ENTREZGENE, UniProtKB/TrEMBL
  CAN9_RAT UniProtKB/Swiss-Prot
  F1LR50 ENTREZGENE
  O35920 ENTREZGENE
UniProt Secondary F1LR50 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-29 Capn9  calpain 9  Capn9  calpain 9 (nCL-4)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Capn9  calpain 9 (nCL-4)      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference