Casq1 (calsequestrin 1) - Rat Genome Database

Name: Casq1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Casq1 (calsequestrin 1) Rattus norvegicus

Analyze

Symbol:

Casq1

Name:

calsequestrin 1

RGD ID:

1586677

Description:

Enables calcium ion binding activity. Involved in several processes, including regulation of sequestering of calcium ion; response to denervation involved in regulation of muscle adaptation; and skeletal muscle tissue development. Located in I band; T-tubule; and terminal cisterna lumen. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human CASQ1 (calsequestrin 1); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

Aspartactin; calsequestrin 1 (fast-twitch, skeletal muscle); calsequestrin, skeletal muscle isoform; Calsequestrin-1; Laminin-binding protein; LOC686019; similar to Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)

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):	CASQ1 (calsequestrin 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Casq1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Casq1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CASQ1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CASQ1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Casq1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CASQ1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CASQ1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Casq1 (calsequestrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	ZNF281 (zinc finger protein 281)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	CASQ1 (calsequestrin 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Casq1 (calsequestrin 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	casq1a (calsequestrin 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	casq1b (calsequestrin 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	csq-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	casq1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

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	13	87,203,021 - 87,212,710 (-)	NCBI		GRCr8
mRatBN7.2	13	84,670,648 - 84,680,339 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	84,670,649 - 84,680,339 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	13	87,173,972 - 87,183,660 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	88,574,232 - 88,583,921 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	85,758,977 - 85,768,666 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	90,592,676 - 90,602,365 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	90,592,681 - 90,602,365 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	13	95,113,781 - 95,123,470 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	88,200,506 - 88,210,418 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	13	84,282,072 - 84,291,712 (-)	NCBI		Celera
Cytogenetic Map	13	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autoimmune interstitial lung, joint, and kidney disease (ISO)

Experimental Diabetes Mellitus (IEP)

familial hemiplegic migraine (ISO)

gastrointestinal stromal tumor (ISO)

genetic disease (ISO)

malignant hyperthermia (ISO)

myopathy (ISO)

parathyroid carcinoma (ISO)

peroxisome biogenesis disorder 12A (ISO)

type 2 diabetes mellitus (ISO)

Vacuolar Myopathy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3,4-methylenedioxymethamphetamine (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

CGP 52608 (ISO)

chlordecone (ISO)

chromium atom (ISO)

cobalt dichloride (EXP)

copper atom (EXP)

copper(0) (EXP)

diuron (EXP)

doxorubicin (ISO)

endosulfan (EXP)

ethanol (EXP)

furan (EXP)

genistein (EXP)

glycidol (EXP)

metformin (EXP)

nicotinic acid (ISO)

ozone (ISO)

paraquat (EXP)

pioglitazone (ISO)

rotenone (EXP)

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

silicon dioxide (ISO)

sodium fluoride (EXP)

sodium nitrate (ISO)

sunitinib (ISO)

triclosan (ISO)

triptonide (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

endoplasmic reticulum organization (ISO)

positive regulation of release of sequestered calcium ion into cytosol (ISO,ISS)

protein polymerization (ISO,ISS)

regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (ISO)

regulation of sequestering of calcium ion (IDA)

regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (IBA,ISO,ISS)

regulation of store-operated calcium entry (ISO,ISS)

response to denervation involved in regulation of muscle adaptation (IEP)

response to heat (ISO)

response to muscle inactivity (IEP)

response to organic substance (IEP)

sarcomere organization (ISO,ISS)

skeletal muscle tissue development (IEP)

Cellular Component

endoplasmic reticulum (ISO)

I band (IDA)

mitochondrial matrix (ISO,ISS)

myofibril (IDA)

sarcolemma (IDA)

sarcoplasmic reticulum (IDA,ISO)

sarcoplasmic reticulum lumen (IBA,ISO,ISS)

sarcoplasmic reticulum membrane (IEA)

T-tubule (IDA)

terminal cisterna (IDA)

terminal cisterna lumen (IDA)

Z disc (IBA)

Molecular Function

calcium ion binding (IBA,IDA,ISO)

identical protein binding (ISO,ISS)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

calcium/calcium-mediated signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Anesthetic- and heat-induced sudden death in calsequestrin-1-knockout mice.	Dainese M, etal., FASEB J. 2009 Jun;23(6):1710-20. doi: 10.1096/fj.08-121335. Epub 2009 Feb 23.
2.	Calsquestrin 1 (CASQ1) gene polymorphisms under chromosome 1q21 linkage peak are associated with type 2 diabetes in Northern European Caucasians.	Das SK, etal., Diabetes. 2004 Dec;53(12):3300-6.
3.	Early effects of denervation on Ca(2+)-handling proteins in skeletal muscle.	Donoghue P, etal., Int J Mol Med. 2004 Jun;13(6):767-72.
4.	Polymorphism in the calsequestrin 1 (CASQ1) gene on chromosome 1q21 is associated with type 2 diabetes in the old order Amish.	Fu M, etal., Diabetes. 2004 Dec;53(12):3292-9.
5.	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.
6.	Taurine supplementation increases skeletal muscle force production and protects muscle function during and after high-frequency in vitro stimulation.	Goodman CA, etal., J Appl Physiol. 2009 Jul;107(1):144-54. Epub 2009 May 7.
7.	Assembly of the sarcoplasmic reticulum. Synthesis of calsequestrin and the Ca2+ + Mg2+ -adenosine triphosphatase on membrane-bound polyribosomes.	Greenway DC and MacLennan DH, Can J Biochem. 1978 Jun;56(6):452-6.
8.	Type 2 diabetes susceptibility genes on chromosome 1q21-24.	Hasstedt SJ, etal., Ann Hum Genet. 2008 Mar;72(Pt 2):163-9.
9.	Calsequestrin expression and calcium binding is increased in streptozotocin-induced diabetic rat skeletal muscle though not in cardiac muscle.	Howarth FC, etal., Pflugers Arch. 2002 May;444(1-2):52-8. Epub 2002 Feb 7.
10.	Expression of endoplasmic reticulum stress proteins during skeletal muscle disuse atrophy.	Hunter RB, etal., Am J Physiol Cell Physiol. 2001 Oct;281(4):C1285-90.
11.	Ultrastructural localization of calsequestrin in rat skeletal muscle by immunoferritin labeling of ultrathin frozen sections.	Jorgensen AO, etal., J Cell Biol. 1983 Nov;97(5 Pt 1):1573-81.
12.	Membrane associated Ca2+ buffers in the heart.	Lee D and Michalak M, BMB Rep. 2010 Mar;43(3):151-7.
13.	Calsequestrin content and SERCA determine normal and maximal Ca2+ storage levels in sarcoplasmic reticulum of fast- and slow-twitch fibres of rat.	Murphy RM, etal., J Physiol. 2009 Jan 15;587(Pt 2):443-60. Epub 2008 Nov 24.
14.	Restricted distribution of mRNAs encoding a sarcoplasmic reticulum or transverse tubule protein in skeletal myofibers.	Nissinen M, etal., J Histochem Cytochem. 2005 Feb;53(2):217-27.
15.	Site-directed mutagenesis and deletion of three phosphorylation sites of calsequestrin of skeletal muscle sarcoplasmic reticulum. Effects on intracellular targeting.	Nori A, etal., Exp Cell Res. 2000 Oct 10;260(1):40-9.
16.	Ca2+-regulatory muscle proteins in the alcohol-fed rat.	Ohlendieck K, etal., Metabolism. 2003 Sep;52(9):1102-12.
17.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
18.	Comprehensive gene review and curation	RGD comprehensive gene curation
19.	Studies of association of the CASQ1 rs2275703 polymorphism in relation to type 2 diabetes and related quantitative metabolic traits among 7,088 Danish whites.	Sparso T, etal., Mol Genet Metab. 2007 Nov;92(3):278-82. Epub 2007 Aug 2.
20.	Regulation of calcium binding proteins calreticulin and calsequestrin during differentiation in the myogenic cell line L6.	Tharin S, etal., J Cell Physiol. 1996 Mar;166(3):547-60.

Additional References at PubMed

PMID:3417768	PMID:7945294	PMID:8042990	PMID:8889548	PMID:12419813	PMID:14651853	PMID:14728599	PMID:15057822	PMID:15489334	PMID:16600288	PMID:17627988	PMID:20833797
PMID:22049211	PMID:22337878	PMID:25084748	PMID:27185316	PMID:28895244	PMID:37589058

Genomics

Comparative Map Data

Casq1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	87,203,021 - 87,212,710 (-)	NCBI		GRCr8
mRatBN7.2	13	84,670,648 - 84,680,339 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	84,670,649 - 84,680,339 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	13	87,173,972 - 87,183,660 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	88,574,232 - 88,583,921 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	85,758,977 - 85,768,666 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	90,592,676 - 90,602,365 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	90,592,681 - 90,602,365 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	13	95,113,781 - 95,123,470 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	88,200,506 - 88,210,418 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	13	84,282,072 - 84,291,712 (-)	NCBI		Celera
Cytogenetic Map	13	q24	NCBI

CASQ1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	160,190,575 - 160,201,886 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	160,190,575 - 160,201,886 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	160,160,365 - 160,171,676 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	158,426,989 - 158,438,300 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	156,973,468 - 156,984,752	NCBI
Celera	1	133,229,049 - 133,240,436 (+)	NCBI		Celera
Cytogenetic Map	1	q23.2	NCBI
HuRef	1	131,517,001 - 131,528,390 (+)	NCBI		HuRef
CHM1_1	1	161,555,636 - 161,567,025 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	159,327,652 - 159,338,962 (+)	NCBI		T2T-CHM13v2.0

Casq1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	172,037,461 - 172,047,462 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	172,037,461 - 172,047,435 (-)	Ensembl		GRCm39 Ensembl
GRCm38	1	172,209,894 - 172,219,895 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	172,209,894 - 172,219,868 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	174,140,025 - 174,150,026 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	1	174,047,013 - 174,056,514 (-)	NCBI		MGSCv36	mm8
Celera	1	175,065,863 - 175,075,868 (-)	NCBI		Celera
Cytogenetic Map	1	H3	NCBI
cM Map	1	79.54	NCBI

Casq1
(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_004955468	11,967,678 - 11,978,836 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955468	11,967,678 - 11,978,836 (+)	NCBI	ChiLan1.0	ChiLan1.0

CASQ1
(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	89,650,462 - 89,662,740 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	89,390,428 - 89,402,899 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	135,544,249 - 135,555,545 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	139,465,605 - 139,476,969 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	139,465,605 - 139,476,969 (+)	Ensembl	panpan1.1		panPan2

CASQ1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	38	22,012,060 - 22,020,430 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	38	22,011,060 - 22,020,383 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	38	22,084,775 - 22,093,156 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	38	22,128,163 - 22,136,607 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	38	22,128,165 - 22,134,332 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	38	22,032,897 - 22,041,272 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	38	22,429,210 - 22,437,626 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	38	22,838,952 - 22,847,496 (-)	NCBI		UU_Cfam_GSD_1.0

Casq1
(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_024405058	6,312,524 - 6,324,146 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936740	430,026 - 442,539 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936740	430,367 - 442,468 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CASQ1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	90,276,757 - 90,288,250 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	90,276,752 - 90,288,990 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	98,218,225 - 98,228,665 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CASQ1
(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	20	3,744,921 - 3,759,220 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	3,744,780 - 3,756,435 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	2,802,575 - 2,814,309 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Casq1
(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_004624794	1,050,955 - 1,065,287 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624794	1,054,119 - 1,064,652 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Casq1
23 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	84
Count of miRNA genes:	63
Interacting mature miRNAs:	78
Transcripts:	ENSRNOT00000009344
Prediction methods:	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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	1	101056920	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	1	101056920	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	101056920	Rat
1581570	Eae17	Experimental allergic encephalomyelitis QTL 17	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	13	8897350	101631289	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	20605871	101339738	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	30395351	101056920	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	31241331	93395974	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	31241331	93395974	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	31241331	93395974	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	13	31241331	93395974	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39754544	84754544	Rat
12879444	Bp397	Blood pressure QTL 397			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	45049404	90049404	Rat
12879471	Bp398	Blood pressure QTL 398			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	45514719	90514719	Rat
12879441	Bp396	Blood pressure QTL 396			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	45699983	90699983	Rat
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	46088046	91088046	Rat
71119	Thym2	Thymus enlargement QTL 2	3.8		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	13	46197976	84753113	Rat
1641901	Alcrsp6	Alcohol response QTL 6			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	13	52362171	97362171	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	56056920	101056920	Rat
738026	Lnnr5	Liver neoplastic nodule remodeling QTL 5	3.29		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	59874408	85581182	Rat
12879475	Bp400	Blood pressure QTL 400			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	61825626	106807694	Rat
2293702	Bss34	Bone structure and strength QTL 34	4.61	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	13	65103704	106807694	Rat
2293687	Bss26	Bone structure and strength QTL 26	4.6	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	13	65103704	106807694	Rat
8655945	Rf61	Renal function QTL 61	3.6		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	13	69060519	86800898	Rat
1331783	Bp221	Blood pressure QTL 221	3.72886		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	69060519	86800898	Rat
1300166	Kidm6	Kidney mass QTL 6	3.93		kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	13	69060519	86800898	Rat
8655959	Pur32	Proteinuria QTL 32	8.4		urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	74023918	97213863	Rat
738027	Lnnr6	Liver neoplastic nodule remodeling QTL 6	3.3		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	74862117	85581182	Rat
2293341	Glom15	Glomerulus QTL 15	9.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	13	74862117	101339893	Rat
4889606	Gluco63	Glucose level QTL 63	2.86	0.003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	13	80753256	106807694	Rat

Markers in Region

RH133764

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	84,670,663 - 84,670,843 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	90,592,692 - 90,592,871	NCBI	Rnor6.0
Rnor_5.0	13	95,113,797 - 95,113,976	UniSTS	Rnor5.0
RGSC_v3.4	13	88,200,522 - 88,200,701	UniSTS	RGSC3.4
Celera	13	84,282,088 - 84,282,267	UniSTS
RH 3.4 Map	13	554.8	UniSTS
Cytogenetic Map	13	q24	UniSTS

G64925

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	84,681,014 - 84,681,174 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	90,603,041 - 90,603,200	NCBI	Rnor6.0
Rnor_5.0	13	95,124,146 - 95,124,305	UniSTS	Rnor5.0
RGSC_v3.4	13	88,211,094 - 88,211,253	UniSTS	RGSC3.4
Celera	13	84,292,388 - 84,292,547	UniSTS
Cytogenetic Map	13	q24	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							8	11					8
Medium		43	7	2	2	2				8	6	7
Low	3		28	17	17	17			74	27	35	4
Below cutoff			20	20		20

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001159594	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC095300	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BE109529	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CA334109	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB699232	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473985	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM056035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216689	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224875	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000013	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000009344 ⟹ ENSRNOP00000009344

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	13	84,670,649 - 84,680,339 (-)	Ensembl
Rnor_6.0 Ensembl	13	90,592,681 - 90,602,365 (-)	Ensembl

RefSeq Acc Id:

NM_001159594 ⟹ NP_001153066

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	87,203,021 - 87,212,710 (-)	NCBI
mRatBN7.2	13	84,670,648 - 84,680,339 (-)	NCBI
Rnor_6.0	13	90,592,676 - 90,602,365 (-)	NCBI
Rnor_5.0	13	95,113,781 - 95,123,470 (-)	NCBI
RGSC_v3.4	13	88,200,506 - 88,210,418 (-)	RGD
Celera	13	84,282,072 - 84,291,712 (-)	RGD

Sequence:

show sequence

GTTGCTCCAGGACCCAGCAGTGTCCACTGTCCACTGCTCTGGCCCACTCTCTACCCCACCCCCA
CCCGGAGCCCCTAACTCAGGACTCTGTATCCGGGGGCTCCTCCCTATTCCAGCTAACCTCCTCT
GGACCAGGAGAGCAGACCCAGCTCGTACTACCTCCATGAGAGCCACTGACAGGATGGGGGCCAG
GGCAGTGTCCAAGCTGCGGCTGGCACTGCTGTTTGTACTGGTGCTAGGGACGCCCAGGTCAGGG
GTCCAGGGGGAGGACGGGCTGGACTTCCCTGAATACGACGGTGTGGACCGCGTGATCAATGTGA
ACGCAAAGAACTACAAGAACGTGTTTAAGAAGTATGAGGTGCTAGCCCTCCTCTACCATGAGCC
CCCCGAGGACGACAAGGCCTCCCAAAGACAATTTGAGATGGAGGAGCTAATTCTGGAGTTAGCA
GCCCAAGTCCTAGAAGACAAGGGTGTTGGCTTTGGCCTGGTGGACTCTGAGAAAGATGCAGCTG
TGGCCAAGAAACTAGGCCTAACTGAAGAGGACAGCGTGTATGTGTTCAAAGGAGATGAAGTCAT
CGAGTATGATGGCGAGTTTTCCGCAGACACTTTGGTGGAGTTTCTGCTCGATGTCCTAGAAGAC
CCTGTCGAATTGATTGAAGGTGAACGAGAGCTGCAGGCATTTGAGAACATCGAGGATGAAATCA
AACTCATTGGCTACTTCAAGAGCAAAGACTCAGAGCATTACAAAGCCTACGAGGATGCAGCTGA
AGAATTCCACCCCTACATCCCTTTCTTCGCTACCTTCGACAGCAAGGTGGCAAAGAAGCTGACG
CTGAAGTTGAACGAGATCGATTTCTATGAGGCCTTCATGGAAGAACCTGTGACCATCCCAGACA
AGCCCAACAGTGAAGAGGAGATTGTCAGCTTCGTGGAGGAGCACAGGAGATCGACCCTGAGGAA
ACTGAAGCCTGAGAGTATGTATGAGACTTGGGAGGATGATCTGGATGGAATCCACATTGTGGCC
TTTGCAGAGGAAGCTGACCCTGATGGTTATGAGTTCTTAGAGACTCTCAAGGCTGTGGCCCAAG
ACAACACTGAGAACCCTGACCTCAGTATCATCTGGATTGACCCTGATGACTTCCCACTGCTGGT
CCCGTACTGGGAGAAGACCTTTGACATCGACTTGTCAGCTCCGCAAATAGGAGTTGTCAATGTT
ACGGATGCGGACAGCATATGGATGGAGATGGACGACGAGGAGGACCTTCCTTCTGCTGAGGAGC
TGGAGGACTGGCTGGAGGATGTGCTGGAGGGTGAAATCAACACAGAGGATGACGACGACGACGA
CGACGACGACGATGATGACGACGACGACGACGATGACTAGTTGCTATGGCAACTCCTTACCAGC
CCCCCTTGCTCTTTACATGTACCTTCCTACCGCCCATGCACTGCCCCGAGCTCCTTGGGACACT
AGGTCATTCTCTACTATAGGGCCAACTGTGGTCTACATGCAGGGTGCTCGAGATCCTGGTCTCC
CTCGCTGGAGAAAAGGAGCTGCTTTATCTCCGATACCAGCCCAGTTCTCTCATCTGACTTGTTT
CTTATCCCGTACCTTATCTGTATCTACTGTTTCTCTTCTACCACTCCCCATACTTAACGATTTG
CAAACTCTTCTCTGTCCCTTCCATCGGTACAGTCTCCCATTACTCAAATCTTAAACCTTTCCGA
CTGTCCTGACCCTGGCTAGGAGGAAGGGAGGTACTGTGTTAGGGGCTATATCTTAGCCATCTCC
TGTTAATGTATTTGGGTCAAATGCAAGGCCTTAATAAAGAAATCTGGGGCAGAATGAAAAAAAA
AAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001153066	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94693	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000009344
	ENSRNOP00000009344.5
	ENSRNOP00055030267
	ENSRNOP00060030769
	ENSRNOP00065036719
GenBank Protein	P19633	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_001153066 ⟸ NM_001159594
- Peptide Label:	precursor
- UniProtKB:	P19633 (UniProtKB/Swiss-Prot), A6JG37 (UniProtKB/TrEMBL)
- Sequence:	show sequence MRATDRMGARAVSKLRLALLFVLVLGTPRSGVQGEDGLDFPEYDGVDRVINVNAKNYKNVFKKY EVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEEDS VYVFKGDEVIEYDGEFSADTLVEFLLDVLEDPVELIEGERELQAFENIEDEIKLIGYFKSKDSE HYKAYEDAAEEFHPYIPFFATFDSKVAKKLTLKLNEIDFYEAFMEEPVTIPDKPNSEEEIVSFV EEHRRSTLRKLKPESMYETWEDDLDGIHIVAFAEEADPDGYEFLETLKAVAQDNTENPDLSIIW IDPDDFPLLVPYWEKTFDIDLSAPQIGVVNVTDADSIWMEMDDEEDLPSAEELEDWLEDVLEGE INTEDDDDDDDDDDDDDDDDDD hide sequence

RefSeq Acc Id:

ENSRNOP00000009344 ⟸ ENSRNOT00000009344

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P19633-F1-model_v2	AlphaFold	P19633	1-406	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699022

Promoter ID:

EPDNEW_R9547

Type:

multiple initiation site

Name:

Casq1_1

Description:

calsequestrin 1

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	13	90,602,369 - 90,602,429	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1586677	AgrOrtholog
BioCyc Gene	G2FUF-17328	BioCyc
Ensembl Genes	ENSRNOG00000006930	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00055021713	UniProtKB/Swiss-Prot
	ENSRNOG00060021516	UniProtKB/Swiss-Prot
	ENSRNOG00065026007	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000009344	ENTREZGENE
	ENSRNOT00000009344.7	UniProtKB/Swiss-Prot
	ENSRNOT00055037180	UniProtKB/Swiss-Prot
	ENSRNOT00060037296	UniProtKB/Swiss-Prot
	ENSRNOT00065044825	UniProtKB/Swiss-Prot
Gene3D-CATH	Glutaredoxin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Calsequestrin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Calsequestrin_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Calsequestrin_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Calsequestrin_middle_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Calsequestrin_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Thioredoxin-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:686019	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	686019	ENTREZGENE
PANTHER	CALSEQUESTRIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CALSEQUESTRIN-1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Calsequestrin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	CASQ1	RGD
PhenoGen	Casq1	PhenoGen
PRINTS	CALSEQUESTRN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CALSEQUESTRIN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CALSEQUESTRIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000006930	RatGTEx
	ENSRNOG00055021713	RatGTEx
	ENSRNOG00060021516	RatGTEx
	ENSRNOG00065026007	RatGTEx
Superfamily-SCOP	SSF52833	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6JG37	ENTREZGENE, UniProtKB/TrEMBL
	CASQ1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-12-09	Casq1	calsequestrin 1	Casq1	calsequestrin 1 (fast-twitch, skeletal muscle)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-18	Casq1	calsequestrin 1 (fast-twitch, skeletal muscle)	Casq1	calsequestrin 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-07-08	Casq1	calsequestrin 1	LOC679341	similar to Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)	Data merged from RGD:1589531	1643240	APPROVED
2008-03-05	Casq1	calsequestrin 1	LOC686019	similar to Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-19	LOC686019	similar to Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-19	LOC679341	similar to Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)			Symbol and Name status set to provisional	70820	PROVISIONAL

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 - CTD

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