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Gene: Capn9 (calpain 9) Rattus norvegicus

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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. Biomarker of hypertension. 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

Alliance Orthologs

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):	CAPN9 (calpain 9)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Capn9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Capn9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CAPN9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CAPN9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Capn9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CAPN9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CAPN9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Capn9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Capn9 (calpain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CAPN9 (calpain 9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Capn9 (calpain 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	capn9 (calpain 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CalpA	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CalpA	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clp-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clp-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clp-7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clp-3	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	capn9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	capn9	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	19	69,446,847 - 69,483,810 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	19	69,446,847 - 69,483,810 (+)	Ensembl				GRCr8
mRatBN7.2	19	52,549,448 - 52,586,413 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	52,549,448 - 52,586,413 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	19	59,334,438 - 59,371,384 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	60,186,063 - 60,223,037 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	62,260,893 - 62,297,832 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	57,341,938 - 57,378,901 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	57,341,938 - 57,378,901 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	19	68,047,157 - 68,084,264 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	19	54,759,009 - 54,796,390 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	19	51,919,286 - 51,955,889 (+)	NCBI		Celera
RGSC_v3.1	19	54,763,943 - 54,801,111 (+)	NCBI
Cytogenetic Map	19	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hypertension (IEP)

stomach cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

acetamide (EXP)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

diethylstilbestrol (ISO)

dimethylarsinic acid (EXP)

diuron (EXP)

endosulfan (EXP)

entinostat (ISO)

folic acid (ISO)

genistein (ISO)

lipopolysaccharide (ISO)

methapyrilene (ISO)

N,N-diethyl-m-toluamide (EXP)

N-nitrosodiethylamine (ISO)

p-menthan-3-ol (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

permethrin (EXP)

phorbol 13-acetate 12-myristate (ISO)

progesterone (ISO)

resveratrol (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

testosterone (ISO)

thimerosal (ISO)

trichloroethene (EXP)

urethane (ISO)

valproic acid (ISO)

zearalenone (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

proteolysis (IBA,IEA)

Cellular Component

cytoplasm (IBA)

Molecular Function

calcium ion binding (IEA,TAS)

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

cysteine-type peptidase activity (IEA)

hydrolase activity (IEA)

metal ion binding (IEA)

peptidase activity (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	19	69,446,847 - 69,483,810 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	19	69,446,847 - 69,483,810 (+)	Ensembl				GRCr8
mRatBN7.2	19	52,549,448 - 52,586,413 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	52,549,448 - 52,586,413 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	19	59,334,438 - 59,371,384 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	60,186,063 - 60,223,037 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	62,260,893 - 62,297,832 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	57,341,938 - 57,378,901 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	57,341,938 - 57,378,901 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	19	68,047,157 - 68,084,264 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	19	54,759,009 - 54,796,390 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	19	51,919,286 - 51,955,889 (+)	NCBI		Celera
RGSC_v3.1	19	54,763,943 - 54,801,111 (+)	NCBI
Cytogenetic Map	19	q12	NCBI

CAPN9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	230,747,388 - 230,801,989 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	230,747,348 - 230,804,397 (+)	Ensembl			hg38	GRCh38
GRCh37	1	230,883,134 - 230,937,735 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	228,949,753 - 229,004,372 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	227,189,864 - 227,244,253	NCBI
Celera	1	204,149,151 - 204,203,730 (+)	NCBI		Celera
Cytogenetic Map	1	q42.2	NCBI
HuRef	1	201,367,929 - 201,422,446 (+)	NCBI		HuRef
CHM1_1	1	232,156,149 - 232,210,762 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	230,127,941 - 230,182,452 (+)	NCBI		T2T-CHM13v2.0

Capn9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	125,301,361 - 125,345,470 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	125,302,850 - 125,345,470 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	8	124,576,062 - 124,618,731 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	124,576,111 - 124,618,731 (+)	Ensembl			mm10	GRCm38
MGSCv37	8	127,100,011 - 127,142,631 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	8	127,462,201 - 127,504,812 (+)	NCBI		MGSCv36	mm8
Celera	8	128,879,934 - 128,910,507 (+)	NCBI		Celera
Cytogenetic Map	8	E2	NCBI
cM Map	8	72.81	NCBI

Capn9
(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_004955492	7,809,188 - 7,845,090 (-)	Ensembl
ChiLan1.0	NW_004955492	7,809,188 - 7,845,090 (-)	NCBI	ChiLan1.0	ChiLan1.0

CAPN9
(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	1	18,411,108 - 18,459,432 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	18,602,251 - 18,651,772 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	206,297,088 - 206,347,427 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	211,324,405 - 211,378,944 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	211,324,405 - 211,378,944 (+)	Ensembl			panPan2	panpan1.1

CAPN9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	8,613,222 - 8,653,534 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	8,612,682 - 8,653,467 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	8,604,905 - 8,645,249 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	4	8,637,647 - 8,677,873 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	4	8,637,107 - 8,678,521 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	4	8,641,831 - 8,682,029 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	4	8,763,717 - 8,803,940 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	4	8,993,883 - 9,034,136 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Capn9
(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	NW_024409344	43,506,573 - 43,534,017 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936484	19,671,964 - 19,699,161 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936484	19,671,799 - 19,699,161 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CAPN9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	59,582,046 - 59,623,376 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	14	59,581,999 - 59,623,553 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	64,246,812 - 64,288,645 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CAPN9
(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	25	68,018,785 - 68,072,299 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	68,019,375 - 68,072,123 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666055	69,925,003 - 69,973,406 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Capn9
(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_004624775	18,790,527 - 18,826,830 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624775	18,792,599 - 18,827,082 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Capn9
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	17	44,101,643 - 44,137,846 (+)	NCBI		Rrattus_CSIRO_v1

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2313395	Anxrr26	Anxiety related response QTL 26			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	19	44385134	74246245	Rat
1578764	Stresp19	Stress response QTL 19	3.6	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	19	32539615	74246245	Rat
5135224	Leukc1	Leukocyte quantity QTL 1			eosinophil quantity (VT:0002602)	blood eosinophil count (CMO:0000033)	19	61249161	74246245	Rat
1331788	Rf45	Renal function QTL 45	2.818		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	19	31777888	74246245	Rat
631840	Niddm38	Non-insulin dependent diabetes mellitus QTL 38	3.86		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	19	10329076	74246245	Rat
724546	Kidm3	Kidney mass QTL 3	3.1		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	19	46226778	74246245	Rat
7247442	Uae39	Urinary albumin excretion QTL 39			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	2194317	74246245	Rat
7411549	Bw130	Body weight QTL 130	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	32365311	74246245	Rat
1549835	Tcas7	Tongue tumor susceptibility QTL 7		0.001	tongue integrity trait (VT:0010553)	squamous cell carcinoma of the head and neck tumor number (CMO:0001876)	19	41722546	74246245	Rat
1331737	Uae29	Urinary albumin excretion QTL 29	5.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	36289	74246245	Rat
724566	Uae12	Urinary albumin excretion QTL 12	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	2194317	74246245	Rat
61423	Cia14	Collagen induced arthritis QTL 14	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	19	10833618	74246245	Rat

Markers in Region

RH137412

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	52,586,202 - 52,586,416 (+)	MAPPER	mRatBN7.2
Rnor_6.0	19	57,378,691 - 57,378,904	NCBI	Rnor6.0
Rnor_5.0	19	68,084,054 - 68,084,267	UniSTS	Rnor5.0
RGSC_v3.4	19	54,796,180 - 54,796,393	UniSTS	RGSC3.4
RH 3.4 Map	19	721.8	UniSTS
Cytogenetic Map	19	q12	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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	1	17	62	38	39	16	37	16	5	117	70	8	43	15	48	23	9	9

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001271140	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC125724	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U89514	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000025357 ⟹ ENSRNOP00000025357

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	19	69,446,847 - 69,483,810 (+)	Ensembl
mRatBN7.2 Ensembl	19	52,549,448 - 52,586,413 (+)	Ensembl
Rnor_6.0 Ensembl	19	57,341,938 - 57,378,901 (+)	Ensembl

RefSeq Acc Id:

NM_001271140 ⟹ NP_001258069

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	19	69,446,847 - 69,483,810 (+)	NCBI
mRatBN7.2	19	52,549,448 - 52,586,413 (+)	NCBI
Rnor_6.0	19	57,341,938 - 57,378,901 (+)	NCBI
Rnor_5.0	19	68,047,157 - 68,084,264 (+)	NCBI
Celera	19	51,919,286 - 51,955,889 (+)	NCBI

Sequence:

show sequence

TTTTCCTCTGCTAGGCTGTGGAGAAGTAGTCATGCCTTACCTGCATCGGTCCCTGAGACCCCAG
CCACAGCCAGTCCCCAGGGATGCCAGGACTGTCCACTCCTCGGGCCACAGCTTTGAGCAGCTGA
GGCAAAGCTGTCTGCAGTCGGGCACCTTGTTTGAGGATGCTGACTTCCCTGCCAGCAATAGTTC
ACTGTTCTACAGCGAGAGGCCCCAGGTCCCCTTTGTGTGGAAGCGGCCAGGGGAAATTGTGGAA
AACCCAGAATTCATTCTGGGAGGGGCCACCAGGACCGACATCTGCCAAGGGGAACTGGGAGACT
GCTGGCTCCTGGCCGCCATTGCCTCCCTAACCCTCAATCAGAAAGCACTGGCCAGAGTGGTACC
CCAGGACCAAGGATTTGGTTCTGGCTATGCTGGGATATTTCACTTCCAGTTCTGGCAGCACAGT
GAGTGGCTGGACGTGGTGATTGATGACCGCCTGCCTACCTTTCGGGATCGCCTGGTCTTCCTCC
ACTCTGCCGACCACAATGAGTTCTGGAGCGCACTGCTGGAGAAAGCCTATGCCAAGCTGAACGG
GAGTTACGAGGCACTGAAGGGGGGCAGCGCCATCGAAGCCATGGAGGACTTCACCGGGGGTGTG
GCTGAGAACTTCCAAATCCGAGAGGCACCAGAGGATTTCTACGAGATTCTGGAGAAGGCCCTGC
GGCGTGGTTCCTTGCTGGGCTGCTCCATAGATACCCTGAATGCCTCAGAATCTGAAGCCCGCAC
ACCTTTGGGCCTCATTAAGGGCCATGCCTACACTGTGACTGGACTCGACCAGGTAAACTTCCAC
GGCCAGAGAATCAAGCTCATCAGAGTCCGTAACCCTTGGGGCCAGGTGGAATGGAACGGGCCAT
GGAGCGACAGCTCTCCTGAGTGGCGCTCCATGAGCCTGGAGGAGCAGAAGCGCCTAGGTCACAC
CGCCCTTGACGATGGAGAATTCTGGATGGCATTTGAGGACTTCAAGACCCATTTTGACAAAGTG
GAGATCTGCAACCTCACGCCTGATGCCCTGGAGGACAACACCCTCCACAAGTGGGAGGTGACCA
TCCACCAAGGAAGCTGGGTTCGTGGCTCCACCGCCGGCGGCTGCCGCAACTTCCTGGACACCTT
CTGGACCAACCCACAGATAAAGCTGTCTCTGACAGAGAGGGATGAGGGCCAGGAGGGCTGCACT
TTCCTAGCAGCCTTGATGCAGAAAGACCGCAGGAGGCTCAAGAGGTTTGGTGCCAACATGCTGA
CCATTGGCTATGCCATTTACCAGTGCCCAGACAAGGACGGACACCTGAATAGGGACTTTTTCAG
GTACCATGCCTCTCTGGCCCGAAGTAAGACATTCATCAACTTGAGAGAAGTCTCAGGCCGCTTC
CAGCTGCCCCCGGGAGACTATATCCTCATCCCCAGCACCTTTGAGCCACACCAGGAGGCTGACT
TCTGCCTGAGAATCTTCTCTGAGAAGAAAGCTGTTACTCAGGACCTGGATGAGAACATAGACAT
TGACCTTCCTGAGCTTCCAAAGCCGACACCACAGGAGGAGGAAACCGAAGAGGAGCGGCAGTTC
CGGGCCCTGTTCCGTCGAATTGCTGGTGAGGACATGGAGGTGTCAGCAGAAGAGCTTGAATATG
TTCTAAATGCTGTTCTGCAAAAGAAAACAGCCCTCAAGTTCAAGAGGCTGAGCCTGCTTTCCTG
CAGAAACATTATCTCCCTGATGGACACCAGCGGCAACGGGAAGATGGAGTTCGAAGAGTTCCGG
GTGTTCTGGGACAAGCTGAGGTACTGGATGGACCTGTTTCTCCAGTTCGATGTGGACAAGTCCG
GCACCATGTCTTCCTATGAGTTGCGGACAGCACTGAAAGCTGCAGGCTTTCAGCTGGGTAGCCA
TCTCCTGCAGCTGATCGTCCTCAGGTATGCAGACGAGAACCTCCAGCTGGATTTCGATGACTAC
CTCAACTGCCTGGTGCGGCTGGAGAATGCGAGCCGGGTGTTCCAGTGTCTCAGTGTGAAGAACA
AGGACTTCATCCATCTCAACATAAACGAGTTCATCAACTTGACCATGAACATCTGAGCTTGCAC
TGACCTGATGCCGTCTGCCCCTCTGATACTCAGCTGCTGGACCATGAACCTCAGAATTTTTATT
GGAGGGCCATCCCGCCCATTGCTCTCTCCCCACTCCACACCACCCTCCTTCCCTCCCTGTCGAG
ATTTAAATCAAAAAGGGATTGGCCATGTTCTCCGATTCAGTGATACTTCTTCTAAGATCATTGC
TCCACAGGAACTCATGGCACTGCCTGTGTCTGTGCTCAGGCCTGGGGTTGCTGTATGCTCCTCC
CTCCACTGCCCCTCCTCCACCAACCGGAGTCCTGGCTTCTGAGTGCTCCAATCATGCTATCAAG
AC

hide 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
GenBank Protein	O35920	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001258069 ⟸ NM_001271140

- UniProtKB:

F1LR50 (UniProtKB/Swiss-Prot), O35920 (UniProtKB/Swiss-Prot), A6KJ12 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPYLHRSLRPQPQPVPRDARTVHSSGHSFEQLRQSCLQSGTLFEDADFPASNSSLFYSERPQVP
FVWKRPGEIVENPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVVPQDQGFGSGYA
GIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSA
IEAMEDFTGGVAENFQIREAPEDFYEILEKALRRGSLLGCSIDTLNASESEARTPLGLIKGHAY
TVTGLDQVNFHGQRIKLIRVRNPWGQVEWNGPWSDSSPEWRSMSLEEQKRLGHTALDDGEFWMA
FEDFKTHFDKVEICNLTPDALEDNTLHKWEVTIHQGSWVRGSTAGGCRNFLDTFWTNPQIKLSL
TERDEGQEGCTFLAALMQKDRRRLKRFGANMLTIGYAIYQCPDKDGHLNRDFFRYHASLARSKT
FINLREVSGRFQLPPGDYILIPSTFEPHQEADFCLRIFSEKKAVTQDLDENIDIDLPELPKPTP
QEEETEEERQFRALFRRIAGEDMEVSAEELEYVLNAVLQKKTALKFKRLSLLSCRNIISLMDTS
GNGKMEFEEFRVFWDKLRYWMDLFLQFDVDKSGTMSSYELRTALKAAGFQLGSHLLQLIVLRYA
DENLQLDFDDYLNCLVRLENASRVFQCLSVKNKDFIHLNINEFINLTMNI

hide sequence

Ensembl 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	19	57,341,934 - 57,341,994	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:70965	AgrOrtholog
BioCyc Gene	G2FUF-5243	BioCyc
Ensembl Genes	ENSRNOG00000018480	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000025357	ENTREZGENE
	ENSRNOT00000025357.8	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.120.380	UniProtKB/Swiss-Prot
	Cysteine proteinases	UniProtKB/Swiss-Prot
	EF-hand	UniProtKB/Swiss-Prot
InterPro	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
	EF-hand-dom_pair	UniProtKB/Swiss-Prot
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot
	EF_hand_dom	UniProtKB/Swiss-Prot
	Papain-like_cys_pep_sf	UniProtKB/Swiss-Prot
	Pept_cys_AS	UniProtKB/Swiss-Prot
	Peptidase_C2_calpain_cat	UniProtKB/Swiss-Prot
KEGG Report	rno:116694	UniProtKB/Swiss-Prot
NCBI Gene	116694	ENTREZGENE
PANTHER	CALPAIN	UniProtKB/Swiss-Prot
	PTHR10183:SF385	UniProtKB/Swiss-Prot
Pfam	Calpain_III	UniProtKB/Swiss-Prot
	Peptidase_C2	UniProtKB/Swiss-Prot
PhenoGen	Capn9	PhenoGen
PRINTS	CALPAIN	UniProtKB/Swiss-Prot
PROSITE	CALPAIN_CAT	UniProtKB/Swiss-Prot
	EF_HAND_1	UniProtKB/Swiss-Prot
	EF_HAND_2	UniProtKB/Swiss-Prot
	THIOL_PROTEASE_CYS	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000018480	RatGTEx
SMART	calpain_III	UniProtKB/Swiss-Prot
	CysPc	UniProtKB/Swiss-Prot
	EFh	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF47473	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

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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