Clstn3 (calsyntenin 3) - Rat Genome Database

Name: Clstn3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Clstn3 (calsyntenin 3) Rattus norvegicus

Analyze

Symbol:

Clstn3

Name:

calsyntenin 3

RGD ID:

621153

Description:

Predicted to have calcium ion binding activity. Predicted to be involved in several processes, including chemical synaptic transmission; positive regulation of protein localization to synapse; and regulation of synapse assembly. Localizes to postsynaptic membrane. Orthologous to human CLSTN3 (calsyntenin 3); INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,2',5,5'-tetrachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

alc-beta; alcadein-beta; calsyntenin-3; Cs3; Cstn3

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

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):	CLSTN3 (calsyntenin 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Clstn3 (calsyntenin 3)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Clstn3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLSTN3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLSTN3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Clstn3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CLSTN3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CLSTN3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Clstn3 (calsyntenin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CLSTN3 (calsyntenin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Clstn3 (calsyntenin 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Cals	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	casy-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	157,331,494 - 157,364,769 (-)	NCBI
Rnor_6.0 Ensembl	4	157,043,925 - 157,078,130 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	157,044,736 - 157,078,013 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	224,064,529 - 224,097,591 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	160,631,047 - 160,665,193 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	160,875,982 - 160,910,129 (-)	NCBI
Celera	4	146,072,428 - 146,105,625 (-)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

developmental and epileptic encephalopathy 21 (ISO)

Hyperphosphatemic Familial Tumoral Calcinosis 1 (ISO)

Klippel-Feil syndrome 3 (ISO)

peroxisome biogenesis disorder 2B (ISO)

Temtamy syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1-naphthyl isothiocyanate (EXP)

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

2,2',5,5'-tetrachlorobiphenyl (EXP)

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

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-diaminodiphenylmethane (ISO)

7,12-dimethyltetraphene (ISO)

acetamide (EXP)

acrylamide (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bromobenzene (EXP)

Butylbenzyl phthalate (EXP)

cadmium dichloride (EXP)

carbon nanotube (ISO)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

dexamethasone (ISO)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP)

dichloroacetic acid (ISO)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

ethanol (ISO)

fenamidone (ISO)

isotretinoin (ISO)

lead(0) (ISO)

lead(2+) (ISO)

mono(2-ethylhexyl) phthalate (ISO)

monosodium L-glutamate (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

permethrin (ISO)

pioglitazone (ISO)

pirinixic acid (ISO)

pravastatin (EXP,ISO)

pregnenolone 16alpha-carbonitrile (ISO)

selenomethionine (ISO)

silver atom (ISO)

silver(0) (ISO)

sunitinib (ISO)

tetrachloromethane (EXP)

titanium dioxide (ISO)

tributylstannane (ISO)

trichloroethene (ISO)

triptonide (ISO)

troglitazone (ISO)

uranium atom (ISO)

valproic acid (ISO)

zaragozic acid A (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chemical synaptic transmission (NAS)

homophilic cell adhesion via plasma membrane adhesion molecules (IEA)

positive regulation of protein localization to synapse (IEA,ISO)

positive regulation of synapse assembly (IBA,IEA,ISO)

positive regulation of synaptic transmission (IBA,IEA,ISO)

regulation of cell growth (IEA,ISO)

regulation of presynapse assembly (IEA,ISO)

synapse assembly (IEA,ISO)

synaptic transmission, GABAergic (IEA,ISO)

synaptic transmission, glutamatergic (IEA,ISO)

Cellular Component

cell projection (IEA)

cell surface (IBA,IEA,ISO)

dendrite (IEA)

endoplasmic reticulum membrane (IEA)

GABA-ergic synapse (IEA,ISO)

glutamatergic synapse (IEA,ISO)

Golgi membrane (IEA)

integral component of postsynaptic density membrane (IEA,ISO)

postsynaptic density (ISO)

postsynaptic membrane (IBA,IDA,ISO)

protein-containing complex (IEA,ISO)

Molecular Function

calcium ion binding (IEA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Hintsch G, etal., Mol Cell Neurosci 2002 Nov;21(3):393-409.
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	RGD automated data pipeline
6.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:18158283	PMID:23376485	PMID:24094106	PMID:24613359

Genomics

Comparative Map Data

Clstn3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	157,331,494 - 157,364,769 (-)	NCBI
Rnor_6.0 Ensembl	4	157,043,925 - 157,078,130 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	157,044,736 - 157,078,013 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	224,064,529 - 224,097,591 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	160,631,047 - 160,665,193 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	160,875,982 - 160,910,129 (-)	NCBI
Celera	4	146,072,428 - 146,105,625 (-)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

CLSTN3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	7,129,698 - 7,158,945 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	7,130,371 - 7,158,945 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	7,282,967 - 7,311,541 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	7,174,234 - 7,202,808 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	7,174,236 - 7,201,985	NCBI
Celera	12	8,859,131 - 8,887,704 (+)	NCBI
Cytogenetic Map	12	p13.31	NCBI
HuRef	12	7,095,705 - 7,124,262 (+)	NCBI		HuRef
CHM1_1	12	7,281,942 - 7,310,507 (+)	NCBI		CHM1_1

Clstn3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	124,407,715 - 124,441,743 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	124,407,540 - 124,441,753 (-)	Ensembl
GRCm38	6	124,430,756 - 124,464,784 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	124,430,581 - 124,464,794 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	124,380,774 - 124,414,802 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	124,396,386 - 124,430,343 (-)	NCBI			mm8
Celera	6	126,121,281 - 126,154,711 (-)	NCBI		Celera
Cytogenetic Map	6	F2	NCBI

Clstn3
(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_004955413	4,690,637 - 4,719,929 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955413	4,690,637 - 4,719,929 (+)	NCBI	ChiLan1.0	ChiLan1.0

CLSTN3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	12	7,175,951 - 7,204,526 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	7,175,951 - 7,204,526 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	7,260,361 - 7,288,903 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CLSTN3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	37,879,047 - 37,913,317 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	37,879,269 - 37,913,281 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	8,703,426 - 8,737,782 (+)	NCBI
ROS_Cfam_1.0	27	38,232,299 - 38,265,672 (-)	NCBI
UMICH_Zoey_3.1	27	38,106,420 - 38,140,738 (-)	NCBI
UNSW_CanFamBas_1.0	27	38,147,404 - 38,181,685 (-)	NCBI
UU_Cfam_GSD_1.0	27	8,181,467 - 8,215,782 (+)	NCBI

Clstn3
(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_024404945	101,963,756 - 102,005,760 (-)	NCBI
SpeTri2.0	NW_004936709	641,615 - 673,309 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLSTN3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	63,572,062 - 63,610,618 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	63,572,062 - 63,612,177 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	65,899,699 - 65,927,179 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLSTN3
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	7,197,725 - 7,226,479 (+)	NCBI
ChlSab1.1 Ensembl	11	7,197,539 - 7,226,651 (+)	Ensembl

Clstn3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624860	3,710,121 - 3,737,617 (+)	NCBI

Position Markers

D4Cebr1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	4	157,061,242 - 157,061,380	NCBI	Rnor6.0
Rnor_5.0	4	224,081,035 - 224,081,173	UniSTS	Rnor5.0
RGSC_v3.4	4	160,647,603 - 160,647,741	UniSTS	RGSC3.4
Celera	4	146,088,912 - 146,089,050	UniSTS
Cytogenetic Map	4	q42	UniSTS

BE101768

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	4	157,074,683 - 157,074,846	NCBI	Rnor6.0
Rnor_5.0	4	224,094,261 - 224,094,424	UniSTS	Rnor5.0
RGSC_v3.4	4	160,661,863 - 160,662,026	UniSTS	RGSC3.4
Celera	4	146,102,295 - 146,102,458	UniSTS
RH 3.4 Map	4	1000.8	UniSTS
Cytogenetic Map	4	q42	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61446	Coreg2	Compensatory renal growth QTL 2	3.5		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	4	147274055	157294090	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	125884464	168047091	Rat
724535	Cm18	Cardiac mass QTL 18	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	4	117926139	162926139	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	131834282	176834282	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	136351734	180689124	Rat
1331759	Hrtrt13	Heart rate QTL 13	3.54628		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	108876717	169215811	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	105971071	168047091	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	63537179	157286626	Rat
631683	Bp116	Blood pressure QTL 116		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	123111827	168111827	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131532269	168047091	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	116726724	157291438	Rat
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	146942075	168998263	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	136351734	174694858	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131532269	168047091	Rat
1581574	Eae20	Experimental allergic encephalomyelitis QTL 20	7.8		nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	152482121	158564471	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	136908430	182878540	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	94893247	168046938	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	145373934	176509907	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	123478354	168478354	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	84475257	178931073	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	4	137171018	182171018	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	7850904	182171018	Rat
1358364	Sradr4	Stress Responsive Adrenal Weight QTL 4	4.92		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	128602727	173602727	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	86438317	168047091	Rat
2303623	Vencon2	Ventilatory control QTL 2	3.8		respiration trait (VT:0001943)	minute ventilation (VE) (CMO:0000132)	4	134917642	179917642	Rat
1549827	Scl46	Serum cholesterol level QTL 46	3.5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	131864442	176864442	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	136351734	174694858	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	132455408	168047091	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
6478720	Alc23	Alcohol consumption QTL 23		0.00509	drinking behavior trait (VT:0001422)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	155386197	184226339	Rat
6478728	Anxrr36	Anxiety related response QTL 36		0.01061	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478733	Anxrr37	Anxiety related response QTL 37		0.00095	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478737	Anxrr38	Anxiety related response QTL 38		0.00159	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	145547014	184226339	Rat
6478757	Anxrr44	Anxiety related response QTL 44		0.01087	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	123587009	168587009	Rat
6478782	Anxrr52	Anxiety related response QTL 52		0.02091	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478785	Anxrr53	Anxiety related response QTL 53		0.01397	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155386197	184226339	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	145547014	184226339	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	145547014	184226339	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	124442168	169442168	Rat
10053718	Scort25	Serum corticosterone level QTL 25	2.15	0.0097	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	156855449	184226339	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	146497452	184226339	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	23850384	169318094	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	112807675	157807675	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146086918	168047091	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	93
Count of miRNA genes:	81
Interacting mature miRNAs:	85
Transcripts:	ENSRNOT00000015570
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.

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			7		1				68
Low	3	20	22	13	15	13	3	3	6	25	40	8	3
Below cutoff		21	24	24	3	24	5	6		9	1	3	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_134376	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC128967	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ431642	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000150	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000015570 ⟹ ENSRNOP00000015570

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	157,043,925 - 157,078,130 (-)	Ensembl

RefSeq Acc Id:

NM_134376 ⟹ NP_599203

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	157,331,494 - 157,364,769 (-)	NCBI
Rnor_6.0	4	157,044,736 - 157,078,013 (-)	NCBI
Rnor_5.0	4	224,064,529 - 224,097,591 (-)	NCBI
RGSC_v3.4	4	160,631,047 - 160,665,193 (-)	RGD
Celera	4	146,072,428 - 146,105,625 (-)	RGD

Sequence:

show sequence

ACCAGCGGGGTCAGCAGGCTTCTTTCTGATCTTGTCCCCGGCCCTCCCCTCGTAGAGTCTCTGC
ATCTCTCCCCCGGGGTGGCATTAGCAGGCTTGAGGCTCCCAGGGGAGAGGAACGCCTGGCCTGG
CGTCCTTAACACCATGACCCTCCTGCTGGTGTCCCTCTTGCTGGCCTCTCTGCTTCAGATCAGC
TCTGGCAACAAAGCGAACAAGCATAAGCCATGGATCGAGGCCGAGTACCAGGGCATCGTCATGG
AGAATGACAACACGGTCCTGTTGAATCCGCCACTCTTTGCCTTGGACAAAGATGCTCCGCTGCG
CTATGCAGGTGAGATCTGTGGCTTCCGGCTCCATGGGTCTGGGGTACCCTTTAAGGCTGTGATC
CTGGACAAGGCAACAGGTGAAGGGCTGATCCGGGCCAAGGAGCCTGTGGACTGCGAGGCCCAGA
AGGAGCACACCTTTACCACCCAGGCTTATGACTGTGTAGATGGGCCCGATGGTGCCAATACCAA
GAAGTCTCACAAGGCGACCGTGCATGTTCGGGTCAACGATGTGAATGAGTTTGCCCCAGTCTTT
GTGGAGCGTCTCTACCGTGCTGCAGTGACTGAGGGGAAGCTGTATGATCGCATCTTACGTGTGG
AAGCCATTGATGGTGACTGCTCCCCTCAGTACAGCCAGATCTGCTACTATGAGATCCTTACACC
CAACACCCCTTTCCTCATTGACAATGATGGCAACATTGAGAACACAGAGAAGTTACAGTACAGT
GGTGAGAAGCTCTATAAGTTCACAGTGACAGCATATGACTGTGGGAAGAAGCGAGCAGCAGATG
ATGCTGAGGTGGAAATCCAGGTGAAGCCCACCTGCAAACCCAGCTGGCAAGGCTGGAACAAAAG
GATTGAATATGCCCCAGGAGCGGGGAGCTTGGCTTTGTTCCCTGGCATCCGCCTGGAGACCTGT
GATGAGCCACTGTGGAACATTCAGGCCACCATAGAGCTGCAGACCAGCCATGTGGCCAAGGGCT
GTGACCGAGACAACTACTCAGAGAGGGCTCTGCGGAAGCTCTGTGGTGCTGCTACTGGGGAGGT
GGACCTGTTGCCCATGCCTGGCCCCAATGCCAACTGGACAGCGGGGCTCTCGGTACACTACAGC
CAGGACAGCAGCCTCATCTACTGGTTCAATGGCACACAAGCTGTGCAAGTTCCCCTGGGTGGTC
CAGCAGGGCTGGGCTCTGGGCCGCAGGATGGCCTCAGTGACCACTTTACCCTGTCTTTCTGGAT
GAAGCATAGTGTGACTCCTAGCAAGGGGAAGAAGGAGGAGGAGACCATTGTATGTAACACCATT
CAGAACGAGGACGGCTACTCTCACTACTCATTGACTGTCCACGGCTGCAGAATCGCCTTTCTCT
ACTGGCCGTTGCTTGAGAGTGCACGCCCGGTCAAGTTCCTCTGGAAGCTGGAGCAGGTATGTGA
CGATGAGTGGCATCACTACGCCCTGAACCTCGAGTTCCCCACAGTCACGCTCTATACTGATGGC
ATCTCCTTCGACCCAGCTCTCATCCACGACAATGGTCTCATCCACCCACCCAGGAGGGAACCTG
CGCTCATGATCGGGGCCTGCTGGTCTGAAGAGAAGAACAAAGAGAAGGAGAAGGGGGGAGAGAA
CAGTACAGACACGACCTCAGGAGACCCCTTGCCGATCCACCATTACTTCCATGGCTACCTAGCT
GGTTTCAGCGTGCGCTCAGGTCGCCTGGAGAGCCGTGAGGTCATCGAGTGCCTCTATGCATGTC
GGGAGGGGCTGGACTATAGGGATTTCGAGAGCCTGGGCAAAGGCATGAAGGTGCACGTGAACCC
CTCGCAGTCCCTGCTCACCTTGGAGGGGGATGATGTGGAGACCTTCAACCATGCCCTGCAGCAC
GTGGCTTACATGAACACTCTGCGCTTTGCCACGCCCGGCGTCAGGCCCCTTCGCCTCACCACCG
CTGTCAAGTGCTTTAGTGAAGAGTCCTGTGTCTCCATCCCTGAAGTGGAGGGCTATGTGGTGGT
TCTTCAGCCCGATGCCCCCCAGATCCTTCTGAGTGGCACAGCTCATTTTGCCCGCCCAGCTGTG
GACTTTGAGGGACCCGAGGGAGTCCCCTTGTTCCCTGATCTTCAGATCACCTGCTCCATTTCTC
ACCAGGTGGAGGCCAAAGCAGATGAGAGTTGGCAGGGCACAGTGACAGACACACGCATGTCAGA
TGAGATTGTACACAACTTGGACGGCTGTGAGATTTCTCTGGTGGGGGATGACCTAGACCCTGAA
CGAGAGAGCCTGCTCTTGGACATGGCTTCCCTGCAGCAGCGAGGCCTGGAACTCACCAACAGAT
CTGCCTACCTCACCATTGCTGGGGTGGAGACCATCACTGTGTATGAAGAGATCCTGAGGCAGGC
TCGTTATCAGCTTCGGCATGGAGCTGCCCTTTATGCCAGGAAATTCCGGCTTTCTTGCTCGGAG
ATGAACGGCCGATACTCCAGCAACGAATTCATTGTGGAGGTCAACGTCCTGCACAGCATGAACC
GGGTGGCCCATCCCAGCCACGTGCTCAGTTCACAGCAGTTCCTGCACCGGGGTCACCAGCCTCC
TCCTGAGATGGCTGGACACAGCCTGGCCAGCTCCCACCGGAACTCCATGGTCCCCAGTGCTGCG
ACTCTCATCATTGTGGTATGCGTGGGCTTTCTGGTGCTTATGGTCATCCTCGGCCTCGTGCGGA
TCCACTCCCTTCATCGCCGTGTCTCAGGAACTGGTGGACCCTCAGGGGCTTCCGCTGACCCGAA
AGACCCTGACCTCTTCTGGGATGACTCTGCTCTCACCATTATCGTGAATCCCATGGAGTCCTAC
CAGAACCAGCAGACTGGTGTGGCAGGGGTTGCTGGTGGCCAGCAAGAGGAAGAGGACAGCAGTG
ATTCCGAAGCAGCTGACTCCCCCAGCAGCGATGAAAGACGCATCATTGAGAGCCCCCCACACCG
CTATTGAGGCT

hide sequence

Protein Sequences


Protein RefSeqs	NP_599203	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAD24292	(Get FASTA)	NCBI Sequence Viewer
	Q8R553	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_599203 ⟸ NM_134376
- Peptide Label:	precursor
- UniProtKB:	Q8R553 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MTLLLVSLLLASLLQISSGNKANKHKPWIEAEYQGIVMENDNTVLLNPPLFALDKDAPLRYAGE ICGFRLHGSGVPFKAVILDKATGEGLIRAKEPVDCEAQKEHTFTTQAYDCVDGPDGANTKKSHK ATVHVRVNDVNEFAPVFVERLYRAAVTEGKLYDRILRVEAIDGDCSPQYSQICYYEILTPNTPF LIDNDGNIENTEKLQYSGEKLYKFTVTAYDCGKKRAADDAEVEIQVKPTCKPSWQGWNKRIEYA PGAGSLALFPGIRLETCDEPLWNIQATIELQTSHVAKGCDRDNYSERALRKLCGAATGEVDLLP MPGPNANWTAGLSVHYSQDSSLIYWFNGTQAVQVPLGGPAGLGSGPQDGLSDHFTLSFWMKHSV TPSKGKKEEETIVCNTIQNEDGYSHYSLTVHGCRIAFLYWPLLESARPVKFLWKLEQVCDDEWH HYALNLEFPTVTLYTDGISFDPALIHDNGLIHPPRREPALMIGACWSEEKNKEKEKGGENSTDT TSGDPLPIHHYFHGYLAGFSVRSGRLESREVIECLYACREGLDYRDFESLGKGMKVHVNPSQSL LTLEGDDVETFNHALQHVAYMNTLRFATPGVRPLRLTTAVKCFSEESCVSIPEVEGYVVVLQPD APQILLSGTAHFARPAVDFEGPEGVPLFPDLQITCSISHQVEAKADESWQGTVTDTRMSDEIVH NLDGCEISLVGDDLDPERESLLLDMASLQQRGLELTNRSAYLTIAGVETITVYEEILRQARYQL RHGAALYARKFRLSCSEMNGRYSSNEFIVEVNVLHSMNRVAHPSHVLSSQQFLHRGHQPPPEMA GHSLASSHRNSMVPSAATLIIVVCVGFLVLMVILGLVRIHSLHRRVSGTGGPSGASADPKDPDL FWDDSALTIIVNPMESYQNQQTGVAGVAGGQQEEEDSSDSEAADSPSSDERRIIESPPHRY hide sequence

RefSeq Acc Id:

ENSRNOP00000015570 ⟸ ENSRNOT00000015570

Protein Domains

Cadherin

Transcriptome

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

Promoters

RGD ID:

13693379

Promoter ID:

EPDNEW_R3904

Type:

single initiation site

Name:

Clstn3_1

Description:

calsyntenin 3

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	4	157,078,109 - 157,078,169	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
4	157057959	157057960	A	T	snv	LEW/Crl (RGD), BBDP/Wor (RGD)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621153	AgrOrtholog
Ensembl Genes	ENSRNOG00000011156	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000015570	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000015570	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Cadherin-like_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cadherin-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Calsyntenin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ConA-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:171393	UniProtKB/Swiss-Prot
NCBI Gene	171393	ENTREZGENE
PANTHER	PTHR14139	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Cadherin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Clstn3	PhenoGen
PRINTS	CADHERIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CADHERIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	SM00112	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49313	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF49899	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	CSTN3_RAT	UniProtKB/Swiss-Prot
	G3V7J1_RAT	UniProtKB/TrEMBL
	Q8R553	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Clstn3	calsyntenin 3	Cstn3		Symbol updated	1299863	APPROVED
2002-08-07	Cstn3	calsyntenin 3			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	highest expression in GABAergic neurons	632523

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