Capn6 (calpain 6) - Rat Genome Database

Name: Capn6
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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. 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

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CAPN6 (calpain 6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Capn6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Capn6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CAPN6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CAPN6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Capn6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CAPN6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CAPN6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Capn6 (calpain 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CAPN6 (calpain 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Capn6 (calpain 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	tra-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	capn6	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	112,177,467 - 112,202,178 (-)	NCBI		GRCr8
mRatBN7.2	X	107,380,774 - 107,405,489 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	107,380,774 - 107,405,489 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	109,518,601 - 109,543,298 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	113,018,304 - 113,043,001 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	110,571,881 - 110,596,588 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	115,049,113 - 115,073,824 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	115,049,154 - 115,073,890 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	113,502,312 - 113,527,023 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	34,697,658 - 34,722,369 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	X	34,751,126 - 34,775,838 (+)	NCBI
Celera	X	106,779,922 - 106,804,635 (-)	NCBI		Celera
Cytogenetic Map	X	q33	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

developmental and epileptic encephalopathy 36 (ISO)

genetic disease (ISO)

hypertension (IEP)

prostate cancer (ISO)

schizophrenia (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

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)

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)

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)

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)

phenylmercury acetate (ISO)

phorbol 13-acetate 12-myristate (ISO)

pirinixic acid (ISO)

progesterone (ISO)

resveratrol (ISO)

rotenone (EXP)

SB 431542 (ISO)

testosterone enanthate (ISO)

titanium dioxide (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

microtubule bundle formation (IEA,ISO,ISS)

proteolysis (IBA,IEA)

regulation of cytoskeleton organization (IEA,ISO,ISS)

Cellular Component

cytoplasm (IBA)

microtubule (ISO)

perinuclear region of cytoplasm (IEA,ISO)

spindle microtubule (IEA,ISO)

Molecular Function

calcium-dependent cysteine-type endopeptidase activity (IBA,IEA)

microtubule binding (IEA,ISO,ISS)

protein binding (ISO)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	112,177,467 - 112,202,178 (-)	NCBI		GRCr8
mRatBN7.2	X	107,380,774 - 107,405,489 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	107,380,774 - 107,405,489 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	109,518,601 - 109,543,298 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	113,018,304 - 113,043,001 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	110,571,881 - 110,596,588 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	115,049,113 - 115,073,824 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	115,049,154 - 115,073,890 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	113,502,312 - 113,527,023 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	34,697,658 - 34,722,369 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	X	34,751,126 - 34,775,838 (+)	NCBI
Celera	X	106,779,922 - 106,804,635 (-)	NCBI		Celera
Cytogenetic Map	X	q33	NCBI

CAPN6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	111,245,099 - 111,270,483 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	111,245,099 - 111,270,483 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	110,488,327 - 110,513,711 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	110,374,987 - 110,400,407 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	X	110,294,475 - 110,319,896	NCBI
Celera	X	110,967,943 - 110,993,390 (-)	NCBI		Celera
Cytogenetic Map	X	q23	NCBI
HuRef	X	100,110,837 - 100,136,321 (-)	NCBI		HuRef
CHM1_1	X	110,399,827 - 110,425,289 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	X	109,693,306 - 109,718,689 (-)	NCBI		T2T-CHM13v2.0

Capn6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	142,585,232 - 142,610,408 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	142,585,227 - 142,610,410 (-)	Ensembl		GRCm39 Ensembl
GRCm38	X	143,802,236 - 143,827,412 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	143,802,231 - 143,827,414 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	140,236,779 - 140,261,955 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	139,048,604 - 139,073,663 (-)	NCBI		MGSCv36	mm8
Celera	X	127,758,391 - 127,783,584 (-)	NCBI		Celera
Cytogenetic Map	X	F2	NCBI
cM Map	X	64.83	NCBI

Capn6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955490	4,499,882 - 4,526,060 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955490	4,499,888 - 4,526,060 (+)	NCBI	ChiLan1.0	ChiLan1.0

CAPN6
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	X	110,738,095 - 110,763,471 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	110,741,706 - 110,767,064 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	100,363,233 - 100,388,631 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	110,822,550 - 110,847,955 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	110,822,170 - 110,848,000 (-)	Ensembl	panpan1.1		panPan2

CAPN6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	84,351,483 - 84,377,365 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	84,351,480 - 84,378,183 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	70,452,893 - 70,478,661 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	X	86,013,239 - 86,039,076 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	X	86,013,232 - 86,039,110 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	X	83,496,162 - 83,521,922 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	X	85,173,775 - 85,199,625 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	X	85,002,271 - 85,028,105 (-)	NCBI		UU_Cfam_GSD_1.0

Capn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	83,597,063 - 83,622,272 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936499	4,035,664 - 4,060,895 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936499	4,041,837 - 4,060,895 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CAPN6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	91,258,688 - 91,288,077 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	91,258,696 - 91,288,128 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	105,673,303 - 105,702,721 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CAPN6
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	99,052,100 - 99,077,508 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	X	99,051,989 - 99,077,302 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666065	24,290,975 - 24,316,307 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Capn6
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624803	4,339,368 - 4,373,298 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624803	4,339,368 - 4,373,400 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Capn6
35 total Variants

miRNA Target Status

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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61430	Cia18	Collagen induced arthritis QTL 18	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	14843113	120568734	Rat
1598837	Memor13	Memory QTL 13	3.2		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	41052407	146860749	Rat
738035	Stresp1	Stress response QTL 1	4.96	0.000011	stress-related behavior trait (VT:0010451)	defensive burying - coping	X	41304447	112935181	Rat
61431	Cia19	Collagen induced arthritis QTL 19	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	65612192	120568734	Rat
724551	Glom1	Glomerulus QTL 1	2.8	0.0004	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	X	75294106	120294106	Rat
1598872	Memor14	Memory QTL 14	4.5		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	93956491	138956491	Rat
738025	Stresp3	Stress response QTL 3	4.61	0.0066	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	100567703	150256146	Rat
1598809	Memor15	Memory QTL 15	4.4		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	103312877	148312877	Rat
1598856	Memor1	Memory QTL 1	1.9		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	X	103312877	148312877	Rat

Markers in Region

RH128245

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	107,380,969 - 107,381,172 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	115,049,309 - 115,049,511	NCBI	Rnor6.0
Rnor_5.0	X	113,502,508 - 113,502,710	UniSTS	Rnor5.0
RGSC_v3.4	X	34,721,971 - 34,722,173	UniSTS	RGSC3.4
Celera	X	106,780,118 - 106,780,320	UniSTS
Cytogenetic Map	X	q14	UniSTS

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		26	6	6		6	2	2	6	20	28		2
Low	1	13	28	22	6	22	6	9	68	15	7	7	6
Below cutoff	2	4	21	12	10	12					6	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031808	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC117954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF067793	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000006638 ⟹ ENSRNOP00000006638

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	107,380,774 - 107,405,489 (-)	Ensembl
Rnor_6.0 Ensembl	X	115,049,154 - 115,073,890 (-)	Ensembl

RefSeq Acc Id:

NM_031808 ⟹ NP_113996

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	X	112,177,467 - 112,202,178 (-)	NCBI
mRatBN7.2	X	107,380,774 - 107,405,489 (-)	NCBI
Rnor_6.0	X	115,049,113 - 115,073,824 (-)	NCBI
Rnor_5.0	X	113,502,312 - 113,527,023 (-)	NCBI
RGSC_v3.4	X	34,697,658 - 34,722,369 (+)	RGD
Celera	X	106,779,922 - 106,804,635 (-)	RGD

Sequence:

show sequence

ATCTTTGTTCAGCTGCGCTGGCTGAACAGACTTAGTGGGGTTACCTGGCTAAGAGCAGCAGCAG
CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAGGGCT
CCTGAGATAACTCAGACCTAGTTGGATAATAATGGGTCCTCCTCTGAAGCTCTTCAAAAACCAG
AAGTACCAAGAACTGAAGCAAGACTGCATGAAGGATGGCCGACTTTTCTGTGACCCTACCTTCC
TACCGGAGAATGATTCTCTGTTTTTCAACCGGCTGCTTCCAGGAAAGGTTGTGTGGAAACGTCC
TCAGGACATTTCTGATGACCCCCATCTGATTGTGGGCAACATTAGCAACCACCAGCTGATCCAG
GGAAGACTGGGGAACAAGGCAATGATTTCTGCATTTTCCTGTTTGGCTGTTCAGGAGTCACACT
GGACAAAGGCGATTCCCAACCATAAGGAACAGGAATGGGATCCTCGAAAGCCAGAAAAATATGC
TGGAATCTTTCGCTTCCGTTTCTGGCATTTTGGAGAATGGACTGAGGTGGTGATTGACGACTTG
CTTCCCACCATCAATGGAGATCTGGTCTTCTCATTCTCCACCTCCATGAATGAGTTTTGGAATG
CTCTACTGGAAAAAGCATATGCAAAGCTTCTGGGCTGTTATGAGGCTTTGGATGGTCTGACCAT
CACTGATATCATCATGGACTTCACGGGCACATTGGCTGAAATCATTGACATGCAGAAAGGACGC
TACACCGATCTTGTTGAGGAGAAGTACAAGCTGTTTGGAGAACTGTACAAAACGTTCACCAAAG
GAGGTCTAATTTCCTGCTCCATTGAGTCTCCCAGCCAGGAGGAACAAGAAGTTGAAACAGATTG
GGGTCTACTGAAGGGTTATACCTACACCATGACTGATATTCGCAAGCTCCGTCTTGGAGAAAGA
CTTGTGGAAGTCTTCAGTACGGAGAAGCTGTATATGGTTCGCCTAAGGAATCCATTGGGAAGAC
AAGAATGGAGCGGCCCCTGGAGTGAAATTTCGGAAGAGTGGCAGCAACTGACTGTAACCGATCG
CAAGAACCTGGGGCTTGTTATGTCTGATGATGGAGAATTTTGGATGAGTCTGGAAGATTTTTGC
CACAACTTTCACAAACTGAATGTCTGCCGCAATGTGAATAACCCTGTTTTCGGTCGCAAGGAGC
TGGAATCAGTGGTGGGATGTTGGACTGTGGATGATGACCCTCTGATGAACCGATCGGGAGGTTG
CTATAACAACCGCGATACCTTCCTGCAGAATCCTCAGTACATCTTCACTGTGCCTGAGGATGGC
CATAAGGTCATCATGTCACTGCAGCAGAAGGATCTACGCACTTACCGCCGAATGGGAAGACCTG
ACAATTACATCATTGGTTTTGAGCTCTTCAAGGTGGAGATGAACCGAAGATTCCGCCTTCATCA
CCTGTATATTCAGGAGCGAGCTGGAACTTCCACCTATATCGACACCCGTACCGTGTTTCTGAGC
AAGTATCTGAAGAAGGGCAACTATGTTCTTGTTCCAACTATGTTCCAGCATGGCCGTACCAGCG
AATTTCTACTGAGGATCTTCTCGGAAGTGCCTGTCCAGCTCAGGGAACTGACATTGGACATGCC
CAAGATGTCTTGCTGGAACCTGGCACGTGGCTACCCAAAGGTGGTTACCCAGATCACTGTCCAC
AGTGCCGAGGGCCTGGAGAAGAAGTATGCCAATGAAACTGTAAATCCATATCTGACCATCAAAT
GTGGAAAGGAAGAAGTCCGTTCTCCTGTCCAGAAGAACACCGTGCATGCCATTTTTGACACCCA
GGCCATTTTCTACCGAAGGACCACTGACATTCCTATTATCATCCAGGTCTGGAATAGCAGAAAA
TTCTGTGATCAGTTCCTGGGGCAGGTTACTCTGGATGCTGACCCCAGTGACTGCCGTGATCTGA
AATCTCTGTATCTGCGTAAGAAGGGTGGTCCCACGGCCAAAGTCAAGCAAGGCCACATCAGTTT
CAAAGTTATCTCTAGCGATGATCTCACTGAGCTCTAAGTATGCATCATCAGAGAATCGTGCCAG
CTTTCCATCATCTGTCAGGCACCAGGTCTTAACCAAGATTCACAATTACTGAAATTCCACACAT
TTATTAACGTTTTCTCTTTTCCGATATTTCCCATACCTCCTGATCCAAGTAGCATCAGTAGCTA
CAGAACCTATATACCTCCAGCAGCTGGACAGGGGAGGTGACAATCCCATCTGGAGATCATACAC
ACACACGTTTACTGAGAAAAGATCCTTAGGGCTTCCAGGGGTGTGAATCAAATGGGACAATAAG
AATCTGACCAGCCTACATGTGTCTTTGCTGTTTCCACCTGCTCAGCTATATCGTGCCCTGTAGG
GCATGTTGGTGAAGGAGAGAGGTGATCAAGGCCAAGCTGGTCTAGCCTGACATCTCAGCTCCTA
ACTGACACTACAGATTTATCAGCAACATTTCACCAGTAGCCAGAGCTGACTTTTTTACCAGTCC
AACCCTATGTCATCATCACCACCACCACCACCTCTGNAAAGTGTGGTCCTGCCCTAACTCAAGT
AACTCCCCCACAGTGTTTTACCTTCATGTTGAGGAAGCTTCCTAGGTGCTTTATCAAGAGCTGG
AGTTCAATGCACCCGAGACAGTGAGAAGGGCTTGAACTTTAGTCATTTGGAAGCCAGCTGTGTG
CCATAAGAGGGAGAAGTTGAAGAAGCTGCAGTGGGAGACAAAGCCTCTGTCCCCCATCCATCCA
CACACACCTACACTCACACACGCGCAGGTAAGCGCGCACGAACTACCATTCAGTCAGTGGGCAA
GAATAAGGACTAGTGAAGAATCATGCACACCGAAAGATGGATGAATCTATTCAGTTATAGGACA
GCCAGTTTGGGGTCCCTGACTACAATGTGAAACCTCTTGCTGCTGCTAGATTTACAAACAAGCC
CATTGCCTTGTGCTTCCTAATATCATTGGTACTGAAAACTCTATATGGGACCTTGAGAGTCTGG
GAACCACCCAGACCCCCCAGGCTTTTCCCTCTGTTCAGAAGCTCCACTCCTCAGGGGTTTGCTT
TTCAGTATGTCTACAAAATTTCCTGTGAACCAGTCATTATATGTTCTTCCCTTCATCCTCATCT
GTCAGTATTCTGCCCCTATTCAAGGCCCAGCATAAATTCCACCTCCTCCATGAAGTTCTTTCAC
ATCTTTTCCCCAAGCCCCACCTCCAACAATATTTCAGTGCTTCTGCAATGATAAAAAAAACATA
GTTGTAGTATTTAGTCTAGTTCAGCATGCACTCATTTAAAAATAACATTTTGTAGCTCTCTCCT
TTTTAACTTACTCATTTTCTATCACATTTTGCTAGTCTTTGTAACTTTTACAGTGCCTTTGCCA
CACTGCCTTACAAACAGAATCACAATAAAGTTCATATTCAAT

hide sequence

Protein Sequences


Protein RefSeqs	NP_113996	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC19367	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000006638
	ENSRNOP00000006638.1
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:

show sequence

MGPPLKLFKNQKYQELKQDCMKDGRLFCDPTFLPENDSLFFNRLLPGKVVWKRPQDISDDPHLI
VGNISNHQLIQGRLGNKAMISAFSCLAVQESHWTKAIPNHKEQEWDPRKPEKYAGIFRFRFWHF
GEWTEVVIDDLLPTINGDLVFSFSTSMNEFWNALLEKAYAKLLGCYEALDGLTITDIIMDFTGT
LAEIIDMQKGRYTDLVEEKYKLFGELYKTFTKGGLISCSIESPSQEEQEVETDWGLLKGYTYTM
TDIRKLRLGERLVEVFSTEKLYMVRLRNPLGRQEWSGPWSEISEEWQQLTVTDRKNLGLVMSDD
GEFWMSLEDFCHNFHKLNVCRNVNNPVFGRKELESVVGCWTVDDDPLMNRSGGCYNNRDTFLQN
PQYIFTVPEDGHKVIMSLQQKDLRTYRRMGRPDNYIIGFELFKVEMNRRFRLHHLYIQERAGTS
TYIDTRTVFLSKYLKKGNYVLVPTMFQHGRTSEFLLRIFSEVPVQLRELTLDMPKMSCWNLARG
YPKVVTQITVHSAEGLEKKYANETVNPYLTIKCGKEEVRSPVQKNTVHAIFDTQAIFYRRTTDI
PIIIQVWNSRKFCDQFLGQVTLDADPSDCRDLKSLYLRKKGGPTAKVKQGHISFKVISSDDLTE
L

hide sequence

RefSeq 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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:70960	AgrOrtholog
BioCyc Gene	G2FUF-1500	BioCyc
Ensembl Genes	ENSRNOG00000004882	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000006638	ENTREZGENE
	ENSRNOT00000006638.4	UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.380	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	2.60.40.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cysteine proteinases	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	C2_Calpain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C2_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C2_domain_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	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
	Papain-like_cys_pep_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_C2_calpain_cat	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:83685	UniProtKB/Swiss-Prot
NCBI Gene	83685	ENTREZGENE
PANTHER	CALPAIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CALPAIN-6	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Calpain_III	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_C2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PF00168	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Capn6	PhenoGen
PRINTS	CALPAIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CALPAIN_CAT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PS50004	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000004882	RatGTEx
SMART	calpain_III	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CysPc	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SM00239	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49562	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF49758	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF54001	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar