Capn6 (calpain 6) - Rat Genome Database

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Gene: Capn6 (calpain 6) Rattus norvegicus
Analyze
Symbol: Capn6
Name: calpain 6
RGD ID: 70960
Description: Predicted to enable microtubule binding activity. Predicted to be involved in microtubule bundle formation and regulation of cytoskeleton organization. Predicted to be located in perinuclear region of cytoplasm and spindle microtubule. Predicted to be active in cytoplasm. Biomarker of hypertension. Orthologous to human CAPN6 (calpain 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calpain-6
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
GRCr8X112,177,467 - 112,202,178 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX112,177,467 - 112,202,178 (-)EnsemblGRCr8
mRatBN7.2X107,380,774 - 107,405,489 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX107,380,774 - 107,405,489 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX109,518,601 - 109,543,298 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X113,018,304 - 113,043,001 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X110,571,881 - 110,596,588 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X115,049,113 - 115,073,824 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX115,049,154 - 115,073,890 (-)Ensemblrn6Rnor6.0
Rnor_5.0X113,502,312 - 113,527,023 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X34,697,658 - 34,722,369 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX106,779,922 - 106,804,635 (-)NCBICelera
RGSC_v3.1X34,751,126 - 34,775,838 (+)NCBI
Cytogenetic MapXq33NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
amphotericin B  (ISO)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
Cuprizon  (EXP)
cyclosporin A  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
glycidol  (EXP)
hydrazine  (ISO)
indometacin  (ISO)
inulin  (ISO)
L-methionine  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
naled  (ISO)
nickel atom  (ISO)
ochratoxin A  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
p-menthan-3-ol  (ISO)
panobinostat  (ISO)
paracetamol  (EXP)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
testosterone enanthate  (ISO)
topiramate  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. 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.
4. Genomic organization of mouse Capn5 and Capn6 genes confirms that they are a distinct calpain subfamily. Matena K, etal., Genomics 1998 Feb 15;48(1):117-20.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Human T-cell leukemia virus type 1 Tax protein stimulates the interferon-responsive enhancer element via NF-kappaB activity. Shimizu T, etal., FEBS Lett 2003 Mar 27;539(1-3):73-7.
Additional References at PubMed
PMID:17210638  


Genomics

Comparative Map Data
Capn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X112,177,467 - 112,202,178 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX112,177,467 - 112,202,178 (-)EnsemblGRCr8
mRatBN7.2X107,380,774 - 107,405,489 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX107,380,774 - 107,405,489 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX109,518,601 - 109,543,298 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X113,018,304 - 113,043,001 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X110,571,881 - 110,596,588 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X115,049,113 - 115,073,824 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX115,049,154 - 115,073,890 (-)Ensemblrn6Rnor6.0
Rnor_5.0X113,502,312 - 113,527,023 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X34,697,658 - 34,722,369 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX106,779,922 - 106,804,635 (-)NCBICelera
RGSC_v3.1X34,751,126 - 34,775,838 (+)NCBI
Cytogenetic MapXq33NCBI
CAPN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X111,245,099 - 111,270,483 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX111,245,099 - 111,270,483 (-)Ensemblhg38GRCh38
GRCh37X110,488,327 - 110,513,711 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X110,374,987 - 110,400,407 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X110,294,475 - 110,319,896NCBI
CeleraX110,967,943 - 110,993,390 (-)NCBICelera
Cytogenetic MapXq23NCBI
HuRefX100,110,837 - 100,136,321 (-)NCBIHuRef
CHM1_1X110,399,827 - 110,425,289 (-)NCBICHM1_1
T2T-CHM13v2.0X109,693,306 - 109,718,689 (-)NCBIT2T-CHM13v2.0
Capn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X142,585,232 - 142,610,408 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX142,585,227 - 142,610,410 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X143,802,236 - 143,827,412 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX143,802,231 - 143,827,414 (-)Ensemblmm10GRCm38
MGSCv37X140,236,779 - 140,261,955 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X139,048,604 - 139,073,663 (-)NCBIMGSCv36mm8
CeleraX127,758,391 - 127,783,584 (-)NCBICelera
Cytogenetic MapXF2NCBI
cM MapX64.83NCBI
Capn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554904,499,882 - 4,526,060 (+)Ensembl
ChiLan1.0NW_0049554904,499,888 - 4,526,060 (+)NCBIChiLan1.0ChiLan1.0
CAPN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X110,738,095 - 110,763,471 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X110,741,706 - 110,767,064 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X100,363,233 - 100,388,631 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X110,822,550 - 110,847,955 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX110,822,170 - 110,848,000 (-)EnsemblpanPan2panpan1.1
CAPN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X84,351,483 - 84,377,365 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX84,351,480 - 84,378,183 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX70,452,893 - 70,478,661 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X86,013,239 - 86,039,076 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX86,013,232 - 86,039,110 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X83,496,162 - 83,521,922 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X85,173,775 - 85,199,625 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X85,002,271 - 85,028,105 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Capn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X83,597,063 - 83,622,272 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364994,035,664 - 4,060,895 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364994,041,837 - 4,060,895 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAPN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX91,258,688 - 91,288,077 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X91,258,696 - 91,288,128 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X105,673,303 - 105,702,721 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CAPN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X99,052,100 - 99,077,508 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX99,051,989 - 99,077,302 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606524,290,975 - 24,316,307 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Capn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248034,339,368 - 4,373,298 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248034,339,368 - 4,373,400 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Capn6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X95,821,940 - 95,839,772 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Capn6
102 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:807
Count of miRNA genes:304
Interacting mature miRNAs:387
Transcripts:ENSRNOT00000006638
Prediction methods:Microtar, Miranda, Pita, 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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X105468858125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat

Markers in Region
RH128245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X107,380,969 - 107,381,172 (+)MAPPERmRatBN7.2
Rnor_6.0X115,049,309 - 115,049,511NCBIRnor6.0
Rnor_5.0X113,502,508 - 113,502,710UniSTSRnor5.0
RGSC_v3.4X34,721,971 - 34,722,173UniSTSRGSC3.4
CeleraX106,780,118 - 106,780,320UniSTS
Cytogenetic MapXq14UniSTS


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
10 12 67 138 89 89 58 23 58 6 278 122 11 118 80 92 31 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000006638   ⟹   ENSRNOP00000006638
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX112,177,467 - 112,202,178 (-)Ensembl
mRatBN7.2 EnsemblX107,380,774 - 107,405,489 (-)Ensembl
Rnor_6.0 EnsemblX115,049,154 - 115,073,890 (-)Ensembl
RefSeq Acc Id: NM_031808   ⟹   NP_113996
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X112,177,467 - 112,202,178 (-)NCBI
mRatBN7.2X107,380,774 - 107,405,489 (-)NCBI
Rnor_6.0X115,049,113 - 115,073,824 (-)NCBI
Rnor_5.0X113,502,312 - 113,527,023 (-)NCBI
RGSC_v3.4X34,697,658 - 34,722,369 (+)RGD
CeleraX106,779,922 - 106,804,635 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_113996 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC19367 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006638
GenBank Protein O88501 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_113996   ⟸   NM_031808
- UniProtKB: O88501 (UniProtKB/Swiss-Prot),   G3V6M4 (UniProtKB/TrEMBL),   A6KG84 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006638   ⟸   ENSRNOT00000006638
Protein Domains
C2   Calpain catalytic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O88501-F1-model_v2 AlphaFold O88501 1-641 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:70960 AgrOrtholog
BioCyc Gene G2FUF-1500 BioCyc
Ensembl Genes ENSRNOG00000004882 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000006638 ENTREZGENE
Gene3D-CATH 2.60.120.380 UniProtKB/Swiss-Prot
  2.60.40.150 UniProtKB/Swiss-Prot
  Cysteine proteinases UniProtKB/Swiss-Prot
InterPro C2_Calpain UniProtKB/Swiss-Prot
  C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  C2_III UniProtKB/Swiss-Prot
  Calpain_cysteine_protease UniProtKB/Swiss-Prot
  Calpain_domain_III UniProtKB/Swiss-Prot
  Calpain_III UniProtKB/Swiss-Prot
  Calpain_III_sf UniProtKB/Swiss-Prot
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot
  Peptidase_C2_calpain_cat UniProtKB/Swiss-Prot
KEGG Report rno:83685 UniProtKB/Swiss-Prot
NCBI Gene 83685 ENTREZGENE
PANTHER CALPAIN UniProtKB/Swiss-Prot
  CALPAIN-6 UniProtKB/Swiss-Prot
Pfam Calpain_III UniProtKB/Swiss-Prot
  Peptidase_C2 UniProtKB/Swiss-Prot
  PF00168 UniProtKB/Swiss-Prot
PhenoGen Capn6 PhenoGen
PRINTS CALPAIN UniProtKB/Swiss-Prot
PROSITE CALPAIN_CAT UniProtKB/Swiss-Prot
  PS50004 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000004882 RatGTEx
SMART calpain_III UniProtKB/Swiss-Prot
  CysPc UniProtKB/Swiss-Prot
  SM00239 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49562 UniProtKB/Swiss-Prot
  SSF49758 UniProtKB/Swiss-Prot
  SSF54001 UniProtKB/Swiss-Prot
UniProt A6KG84 ENTREZGENE, UniProtKB/TrEMBL
  CAN6_RAT UniProtKB/Swiss-Prot
  G3V6M4 ENTREZGENE, UniProtKB/TrEMBL
  O88501 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Capn6  calpain 6      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation downregulated by Tax transformation of Rat-1 fibroblasts, possibly through the CREB/ATF and/or SRF pathways 633613