Ncs1 (neuronal calcium sensor 1) - Rat Genome Database

Name: Ncs1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Ncs1 (neuronal calcium sensor 1) Rattus norvegicus

Analyze

Symbol:

Ncs1

Name:

neuronal calcium sensor 1

RGD ID:

68417

Description:

Enables metal ion binding activity; protein kinase binding activity; and voltage-gated calcium channel activity. Involved in several processes, including positive regulation of calcium-mediated signaling; regulation of exocytosis; and regulation of presynaptic cytosolic calcium ion concentration. Is active in several cellular components, including calyx of Held; postsynaptic cytosol; and presynaptic cytosol. Colocalizes with dense core granule. Orthologous to human NCS1 (neuronal calcium sensor 1); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

Freq; frequenin homolog; frequenin homolog (Drosophila); frequenin-like protein; frequenin-like ubiquitous protein; NCS-1

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):	NCS1 (neuronal calcium sensor 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ncs1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ncs1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NCS1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NCS1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ncs1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NCS1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NCS1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ncs1 (neuronal calcium sensor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NCS1 (neuronal calcium sensor 1)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ncs1 (neuronal calcium sensor 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	ncs1a (neuronal calcium sensor 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	ncs1b (neuronal calcium sensor 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	FRQ1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Frq1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Frq2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ncs-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	ncs1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	3	34,920,949 - 34,966,554 (+)	NCBI		GRCr8
mRatBN7.2	3	14,523,220 - 14,568,829 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	14,523,220 - 14,568,829 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	17,596,129 - 17,641,998 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	26,181,136 - 26,227,007 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	24,428,400 - 24,474,272 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	10,556,250 - 10,602,672 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	10,553,589 - 10,602,672 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	15,911,972 - 15,960,622 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	10,305,202 - 10,354,149 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	10,200,569 - 10,249,517 (+)	NCBI
Celera	3	9,278,946 - 9,324,605 (+)	NCBI		Celera
Cytogenetic Map	3	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

primary coenzyme Q10 deficiency 7 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2-hydroxypropanoic acid (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

ATP (EXP)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

benzoates (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP)

buta-1,3-diene (ISO)

Butylbenzyl phthalate (EXP)

cadmium dichloride (EXP,ISO)

choline (ISO)

cisplatin (ISO)

clofibrate (ISO)

cocaine (ISO)

copper(II) sulfate (ISO)

corticosterone (ISO)

dibutyl phthalate (EXP)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

diquat (ISO)

doxorubicin (ISO)

ethanol (ISO)

fluoranthene (ISO)

folic acid (ISO)

gentamycin (EXP)

glycidyl methacrylate (ISO)

ionomycin (EXP)

ivermectin (ISO)

L-methionine (ISO)

lead(0) (ISO)

menadione (ISO)

methapyrilene (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

phenylarsine oxide (EXP)

phosphatidylinositol 4-phosphate (EXP)

pirinixic acid (ISO)

rac-lactic acid (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

temozolomide (ISO)

triticonazole (EXP)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

wortmannin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

calcium ion transmembrane transport (IEA)

positive regulation of calcium-mediated signaling (IMP)

positive regulation of exocytosis (IDA,IMP)

regulation of neuron projection development (IMP)

regulation of presynaptic cytosolic calcium ion concentration (IDA,IMP)

regulation of synaptic vesicle exocytosis (IDA,IMP)

Cellular Component

axon (ISO)

calyx of Held (IDA,IMP)

cytoplasm (ISO)

cytosol (IEA)

dendrite (ISO)

dense core granule (IDA)

glutamatergic synapse (IDA,IMP)

Golgi apparatus (IEA)

intracellular membrane-bounded organelle (IEA,ISO)

membrane (IEA)

perinuclear region of cytoplasm (IEA)

plasma membrane (ISO)

postsynapse (IDA)

postsynaptic cytosol (IDA)

postsynaptic density (IEA)

presynaptic cytosol (IDA)

Molecular Function

calcium ion binding (IBA,IDA,IEA)

calcium sensitive guanylate cyclase activator activity (IBA,IEA)

calcium-dependent protein kinase inhibitor activity (TAS)

magnesium ion binding (IDA)

protein binding (IPI,ISO)

protein kinase binding (IPI)

voltage-gated calcium channel activity (IMP)

Molecular Pathway Annotations Click to see Annotation Detail View

calcium/calcium-mediated signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Regulatory and structural EF-hand motifs of neuronal calcium sensor-1: Mg 2+ modulates Ca 2+ binding, Ca 2+ -induced conformational changes, and equilibrium unfolding transitions.	Aravind P, etal., J Mol Biol. 2008 Feb 29;376(4):1100-15. doi: 10.1016/j.jmb.2007.12.033. Epub 2007 Dec 23.
2.	Regulation of rhodopsin phosphorylation by a family of neuronal calcium sensors.	De Castro E, etal., Biochem Biophys Res Commun 1995 Nov 2;216(1):133-40.
3.	IL1-receptor accessory protein-like 1 (IL1RAPL1), a protein involved in cognitive functions, regulates N-type Ca2+-channel and neurite elongation.	Gambino F, etal., Proc Natl Acad Sci U S A. 2007 May 22;104(21):9063-8. Epub 2007 May 14.
4.	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.
5.	Analysis of the interacting partners of the neuronal calcium-binding proteins L-CaBP1, hippocalcin, NCS-1 and neurocalcin delta.	Haynes LP, etal., Proteomics. 2006 Mar;6(6):1822-32.
6.	Interaction with neuronal calcium sensor NCS-1 mediates desensitization of the D2 dopamine receptor.	Kabbani N, etal., J Neurosci. 2002 Oct 1;22(19):8476-86.
7.	Mechanisms underlying the neuronal calcium sensor-1-evoked enhancement of exocytosis in PC12 cells.	Koizumi S, etal., J Biol Chem 2002 Aug 16;277(33):30315-24.
8.	Intestinal inflammation modulates expression of the synaptic vesicle protein neuronal calcium sensor-1.	Lourenssen S, etal., Am J Physiol Gastrointest Liver Physiol 2002 Jun;282(6):G1097-104.
9.	The diversity of calcium sensor proteins in the regulation of neuronal function.	McCue HV, etal., Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a004085. doi: 10.1101/cshperspect.a004085. Epub 2010 Jul 28.
10.	Neuronal Ca2+ sensor 1, the mammalian homologue of frequenin, is expressed in chromaffin and PC12 cells and regulates neurosecretion from dense-core granules.	McFerran BW, etal., J Biol Chem. 1998 Aug 28;273(35):22768-72.
11.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
12.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	GOA pipeline	RGD automated data pipeline
14.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
15.	Neuronal calcium sensor-1 binds to regulated secretory organelles and functions in basal and stimulated exocytosis in PC12 cells.	Scalettar BA, etal., J Cell Sci 2002 Jun 1;115(Pt 11):2399-412.
16.	Acute changes in short-term plasticity at synapses with elevated levels of neuronal calcium sensor-1.	Sippy T, etal., Nat Neurosci. 2003 Oct;6(10):1031-8. doi: 10.1038/nn1117. Epub 2003 Aug 31.
17.	Neuronal calcium sensor 1 and phosphatidylinositol 4-OH kinase beta interact in neuronal cells and are translocated to membranes during nucleotide-evoked exocytosis.	Taverna E, etal., J Cell Sci. 2002 Oct 15;115(Pt 20):3909-22.
18.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19.	Neuronal calcium sensor 1 and activity-dependent facilitation of P/Q-type calcium currents at presynaptic nerve terminals.	Tsujimoto T, etal., Science. 2002 Mar 22;295(5563):2276-9. doi: 10.1126/science.1068278.

Additional References at PubMed

PMID:9030700	PMID:10514519	PMID:11825672	PMID:12471042	PMID:12717707	PMID:12783849	PMID:12928444	PMID:14607934	PMID:15336574	PMID:15659215	PMID:16088942	PMID:16469785
PMID:16549499	PMID:16638749	PMID:16691292	PMID:16837555	PMID:17160505	PMID:19656467	PMID:19755107	PMID:20585375	PMID:20838877	PMID:21035569	PMID:22521426	PMID:23376485
PMID:24978930	PMID:25979333	PMID:27796528

Genomics

Comparative Map Data

Ncs1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	34,920,949 - 34,966,554 (+)	NCBI		GRCr8
mRatBN7.2	3	14,523,220 - 14,568,829 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	14,523,220 - 14,568,829 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	17,596,129 - 17,641,998 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	26,181,136 - 26,227,007 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	24,428,400 - 24,474,272 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	10,556,250 - 10,602,672 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	10,553,589 - 10,602,672 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	15,911,972 - 15,960,622 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	10,305,202 - 10,354,149 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	10,200,569 - 10,249,517 (+)	NCBI
Celera	3	9,278,946 - 9,324,605 (+)	NCBI		Celera
Cytogenetic Map	3	p12	NCBI

NCS1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	130,172,404 - 130,237,303 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	130,172,404 - 130,237,303 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	132,934,683 - 132,999,582 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	131,974,678 - 132,038,727 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	130,014,410 - 130,078,457	NCBI
Celera	9	103,585,939 - 103,651,680 (+)	NCBI		Celera
Cytogenetic Map	9	q34.11	NCBI
HuRef	9	102,534,885 - 102,599,998 (+)	NCBI		HuRef
CHM1_1	9	133,083,844 - 133,148,450 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	142,377,132 - 142,442,184 (+)	NCBI		T2T-CHM13v2.0

Ncs1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	31,135,766 - 31,186,001 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	31,135,835 - 31,186,001 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	31,245,708 - 31,295,989 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	31,245,823 - 31,295,989 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	31,101,443 - 31,150,992 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	31,067,932 - 31,117,481 (+)	NCBI		MGSCv36	mm8
MGSCv36	2	31,588,257 - 31,638,499 (+)	NCBI		MGSCv36	mm8
Celera	2	30,984,573 - 30,999,665 (+)	NCBI		Celera
Cytogenetic Map	2	B	NCBI
cM Map	2	21.81	NCBI

Ncs1
(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	NW_004955513	268,979 - 289,385 (+)	NCBI	ChiLan1.0	ChiLan1.0

NCS1
(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	11	9,112,064 - 9,176,572 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	9,114,408 - 9,179,021 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	101,299,724 - 101,364,897 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	129,950,921 - 130,016,257 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	129,950,921 - 130,016,257 (+)	Ensembl	panpan1.1		panPan2

NCS1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	53,661,361 - 53,676,925 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	53,672,910 - 53,676,910 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	52,857,022 - 52,906,752 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	54,558,680 - 54,608,458 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	9	53,334,722 - 53,385,113 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	53,656,911 - 53,706,612 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	53,749,027 - 53,798,770 (-)	NCBI		UU_Cfam_GSD_1.0

Ncs1
(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_024404947	197,522,579 - 197,564,271 (+)	NCBI		HiC_Itri_2

NCS1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	270,274,562 - 270,334,907 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	270,274,504 - 270,334,908 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	304,146,318 - 304,207,069 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NCS1
(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	12	7,910,495 - 7,975,650 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666079	7,474,591 - 7,539,893 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ncs1
(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_004624760	5,376,634 - 5,410,473 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624760	5,374,211 - 5,410,550 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Ncs1
431 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	224
Count of miRNA genes:	156
Interacting mature miRNAs:	174
Transcripts:	ENSRNOT00000011648
Prediction methods:	Microtar, Miranda, Rnahybrid
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
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	27494778	Rat
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	31158234	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	33230976	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	33278763	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	36847613	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	38710544	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	39874793	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	8227194	33703538	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	8227194	47233430	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	8658162	27494778	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	8658162	27494778	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	10778704	50302886	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	10778704	50302886	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	10778823	30356773	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat

Markers in Region

D3Rat194

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	14,529,381 - 14,529,570 (-)	MAPPER	mRatBN7.2
Rnor_6.0	3	10,596,322 - 10,596,510	NCBI	Rnor6.0
Rnor_5.0	3	15,954,272 - 15,954,460	UniSTS	Rnor5.0
RGSC_v3.4	3	10,311,364 - 10,311,552	UniSTS	RGSC3.4
RGSC_v3.4	3	10,311,363 - 10,311,552	RGD	RGSC3.4
RGSC_v3.1	3	10,206,696 - 10,207,022	RGD
SHRSP x BN Map	3	3.5299	UniSTS
SHRSP x BN Map	3	3.5299	RGD
Cytogenetic Map	3	p12	UniSTS

D3Rat232

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	14,529,365 - 14,529,588 (-)	MAPPER	mRatBN7.2
Rnor_6.0	3	10,596,304 - 10,596,526	NCBI	Rnor6.0
Rnor_5.0	3	15,954,254 - 15,954,476	UniSTS	Rnor5.0
RGSC_v3.4	3	10,311,347 - 10,311,570	RGD	RGSC3.4
RGSC_v3.4	3	10,311,348 - 10,311,570	UniSTS	RGSC3.4
RGSC_v3.1	3	10,206,715 - 10,206,938	RGD
Celera	3	9,285,094 - 9,285,324	UniSTS
SHRSP x BN Map	3	3.4899	UniSTS
SHRSP x BN Map	3	3.4899	RGD
Cytogenetic Map	3	p12	UniSTS

AW531469

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	14,568,663 - 14,568,865 (-)	MAPPER	mRatBN7.2
Rnor_6.0	3	10,556,214 - 10,556,415	NCBI	Rnor6.0
Rnor_5.0	3	15,914,587 - 15,914,788	UniSTS	Rnor5.0
RGSC_v3.4	3	10,353,984 - 10,354,185	UniSTS	RGSC3.4
Celera	3	9,324,440 - 9,324,641	UniSTS
RH 3.4 Map	3	50.4	UniSTS
Cytogenetic Map	3	p12	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		34	4	4		4			74	33	24
Low	3	9	31	15	19	15	8	11		2	17	11	8
Below cutoff			21	21		21

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_024366	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L27421	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X82188	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000011648 ⟹ ENSRNOP00000011648

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	10,553,589 - 10,602,672 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000111270 ⟹ ENSRNOP00000091251

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	14,523,220 - 14,568,829 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000115862 ⟹ ENSRNOP00000095238

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	14,556,304 - 14,568,829 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000116110 ⟹ ENSRNOP00000092268

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	14,540,963 - 14,568,829 (+)	Ensembl

RefSeq Acc Id:

NM_024366 ⟹ NP_077342

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	34,920,949 - 34,966,554 (+)	NCBI
mRatBN7.2	3	14,523,220 - 14,568,829 (+)	NCBI
Rnor_6.0	3	10,556,250 - 10,602,672 (-)	NCBI
Rnor_5.0	3	15,911,972 - 15,960,622 (-)	NCBI
RGSC_v3.4	3	10,305,202 - 10,354,149 (+)	RGD
Celera	3	9,278,946 - 9,324,605 (+)	RGD

Sequence:

show sequence

GCTCCCGCTGGGCGCCCCGAGCGGGTCCGGCCCGGGGAGCGGGGGCCGCGGCCGCCGAGCATGG
GGAAATCCAACAGCAAGTTGAAGCCTGAAGTTGTGGAGGAGCTGACCAGAAAAACCTACTTCAC
TGAAAAGGAAGTACAGCAGTGGTACAAGGGTTTCATTAAGGACTGCCCCAGTGGGCAGCTGGAC
GCCGCTGGCTTCCAGAAGATCTACAAACAGTTCTTCCCATTTGGAGACCCCACCAAGTTCGCCA
CGTTTGTTTTCAACGTCTTCGACGAGAACAAGGATGGCAGGATCGAGTTCTCCGAATTCATCCA
GGCTCTATCGGTGACCTCAAGGGGGACCCTGGATGAGAAGTTGAGGTGGGCCTTCAAGCTTTAT
GACTTGGATAACGACGGCTACATCACCAGAAACGAGATGCTGGACATAGTGGATGCCATTTACC
AGATGGTGGGGAACACCGTGGAGCTCCCAGAAGAAGAGAACACACCAGAGAAGAGGGTGGACCG
GATCTTCGCCATGATGGATAAGAACGCTGATGGGAAGCTAACTCTTCAGGAGTTCCAGGAAGGC
TCCAAGGCCGACCCCTCCATTGTGCAGGCGCTGTCCCTCTACGACGGGCTGGTATAGTCCAGGC
CCAGAGCTGTGATGTGTGGGAACCACTAGCCTCTTCCTGTGCCATGAGGCCACCGCAGCCTGAC
ACCACCCCTGTGCCCACCCAGCCTTCCTCGTCTCCACAAAGCCGGCCGCCCTTGAGCCTCCAGG
CCCTGGCTGTCTTTCCCCCAGCCCTGCATCCACCTGCCGCCTGAAGCCACTGGTTCCATCGTCA
ACGACCTCCGCTTGTCCAAACAACGACAACCCAAAACGGAAAGGCTCCAGCCCTCTGCAAACCT
GAGCGCCGGGCTGCCTCCCTCGGCAGCCGTCCCGTTCTTCCTGCTGTCTGGCCTGTGTGCTTTC
TTTTTTCTTTTTTTATTTCAAATGGACAATGTAAAAGAAAACAAACTACCTTCTGTTCTAAAAG
ATACTGACCATTGGGAGAAGGCCTCTGTGTCTCAGAGAACTCAGTCTCTGCCTGGTCCCCTGCA
GTGGTGGCCAGGGGCAGTGAGGCCACTGGCAGGCAAGGGTGTTAGCGGCAGTGACTCACGTGAT
AACAGTATTGTGCATTTTGTGGGGAAACTGAGGGTTTTTTTTTATACTCATACATAATCGATAC
CTTTTATTTATTGGTTGTTAACGAGGCCTGCTACCTTGTGTGTCTGAAACTCCCAGGATGCTGG
GCCTCCGTTTACATGTGCACACCCTCACCCACCTGCCCGCTACACTTGGGAGGATGGTGGCCTG
CAGCGGCCAAGAAGCCAAAAAATCTTTTCCTTTTTTTTTTTTTTTTCTTTCTTTCTCAGATACT
GTGCTCCGTTTTTGGAGAGGGGAAGGTAGGCATTCCTCGATGGCTAATGCACTGTTCCCCCAGC
TTCTGCCCTGGAGCCCCCACCCCTCTCCTCTGCACCCCTTGGAGCCCATAACACTTTTTTTCAA
GAACACACTTGGGGTGTTTTTTGTTTTTTGGTTTTTTTTTTTTTTAATTTTTGCAACTTTACTC
TGATGTTTGCAGCAGAGAAAAGATGGAGAGCCTTGCTCTGGGAGTGGGAACTGGGAGAGGGTGT
CGGGCACACAGAATAGAGTATGAAGTGGGCTTCTCTGGGAACTGCTGGCCTCTGCCTCCTTGAT
GCTAACTAAGGGGCTGGGTAGGTATAGCGTGTGAAC

hide sequence

Protein Sequences


Protein RefSeqs	NP_077342	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA88510	(Get FASTA)	NCBI Sequence Viewer
	CAA57678	(Get FASTA)	NCBI Sequence Viewer
	EDL93277	(Get FASTA)	NCBI Sequence Viewer
	EDL93278	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000091251
	ENSRNOP00000091251.1
	ENSRNOP00000092268.1
	ENSRNOP00000095238.1
	ENSRNOP00055009728
	ENSRNOP00060046809
	ENSRNOP00065029968
GenBank Protein	P62168	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_077342 ⟸ NM_024366
- UniProtKB:	P62168 (UniProtKB/Swiss-Prot), A6JU20 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGKSNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKF ATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAI YQMVGNTVELPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDGLV hide sequence

RefSeq Acc Id:

ENSRNOP00000011648 ⟸ ENSRNOT00000011648

RefSeq Acc Id:

ENSRNOP00000091251 ⟸ ENSRNOT00000111270

RefSeq Acc Id:

ENSRNOP00000092268 ⟸ ENSRNOT00000116110

RefSeq Acc Id:

ENSRNOP00000095238 ⟸ ENSRNOT00000115862

Protein Domains

EF-hand

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P62168-F1-model_v2	AlphaFold	P62168	1-190	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:68417	AgrOrtholog
BioCyc Gene	G2FUF-50180	BioCyc
Ensembl Genes	ENSRNOG00000008761	Ensembl
	ENSRNOG00000064701	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055007375	UniProtKB/Swiss-Prot
	ENSRNOG00060032673	UniProtKB/Swiss-Prot
	ENSRNOG00065021842	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000111270	ENTREZGENE
	ENSRNOT00000111270.1	UniProtKB/Swiss-Prot
	ENSRNOT00000115862.1	UniProtKB/TrEMBL
	ENSRNOT00000116110.1	UniProtKB/TrEMBL
	ENSRNOT00055012276	UniProtKB/Swiss-Prot
	ENSRNOT00060056643	UniProtKB/Swiss-Prot
	ENSRNOT00065037160	UniProtKB/Swiss-Prot
Gene3D-CATH	EF-hand	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	EF-hand-dom_pair	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_hand_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Recoverin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:65153	UniProtKB/Swiss-Prot
NCBI Gene	65153	ENTREZGENE
PANTHER	NEURONAL CALCIUM SENSOR 1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR23055	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	EF-hand_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF-hand_7	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	FREQ	RGD
PhenoGen	Ncs1	PhenoGen
PRINTS	RECOVERIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_HAND_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000008761	RatGTEx
	ENSRNOG00000064701	RatGTEx
	ENSRNOG00055007375	RatGTEx
	ENSRNOG00060032673	RatGTEx
	ENSRNOG00065021842	RatGTEx
SMART	EFh	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF47473	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC205195
UniProt	A0A8I6AM90_RAT	UniProtKB/TrEMBL
	A0A8I6GJM4_RAT	UniProtKB/TrEMBL
	A6JU20	ENTREZGENE, UniProtKB/TrEMBL
	NCS1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	P36610	UniProtKB/Swiss-Prot
	Q9UK26	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-08-02	Ncs1	neuronal calcium sensor 1	Freq	frequenin homolog (Drosophila)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Freq	frequenin homolog (Drosophila)			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_product	member of the EF-hand calcium binding protein superfamily	728740

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)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

RGD Manual Annotations