Syt11 (synaptotagmin 11) - Rat Genome Database

Name: Syt11
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Syt11 (synaptotagmin 11) Rattus norvegicus

Analyze

Symbol:

Syt11

Name:

synaptotagmin 11

RGD ID:

62042

Description:

Predicted to enable several functions, including beta-tubulin binding activity; phosphatidylserine binding activity; and ubiquitin protein ligase binding activity. Involved in negative regulation of cellular component organization and negative regulation of dopamine secretion. Located in several cellular components, including Schaffer collateral - CA1 synapse; inhibitory synapse; and presynaptic active zone membrane. Is integral component of presynaptic active zone membrane. Is active in postsynapse. Is integral component of synaptic vesicle membrane. Orthologous to human SYT11 (synaptotagmin 11); INTERACTS WITH acetamide; ammonium chloride; bis(2-ethylhexyl) phthalate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

synaptotagmin XI; synaptotagmin-11; sytXI

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):	SYT11 (synaptotagmin 11)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Syt11 (synaptotagmin XI)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Syt11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SYT11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SYT11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Syt11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SYT11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SYT11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Syt11 (synaptotagmin 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Syt11 (synaptotagmin XI)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	SYT11 (synaptotagmin 11)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	syt11a (synaptotagmin XIa)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	syt11b (synaptotagmin XIb)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	Syt4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	snt-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)

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
mRatBN7.2	2	174,206,032 - 174,232,540 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	174,206,191 - 174,231,964 (-)	Ensembl
Rnor_6.0	2	188,112,301 - 188,138,180 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	188,112,286 - 188,138,177 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	207,511,186 - 207,537,292 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	180,874,372 - 180,897,792 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	180,823,880 - 180,847,884 (-)	NCBI
Celera	2	168,153,180 - 168,176,598 (-)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

gastrointestinal stromal tumor (ISO)

parathyroid carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

acetamide (EXP)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

anthra[1,9-cd]pyrazol-6(2H)-one (ISO)

aristolochic acid (ISO)

benzo[a]pyrene (ISO)

benzoates (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP,ISO)

Butylbenzyl phthalate (EXP)

cadmium atom (ISO)

chlordecone (ISO)

chlorpyrifos (ISO)

clozapine (EXP)

cocaine (EXP,ISO)

dibutyl phthalate (EXP)

dichlorine (EXP)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

dorsomorphin (ISO)

endosulfan (EXP)

entinostat (ISO)

flutamide (EXP)

folic acid (ISO)

gamma-tocopherol (ISO)

haloperidol (EXP)

levonorgestrel (ISO)

Licochalcone B (ISO)

methylmercury chloride (ISO)

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

nickel atom (ISO)

nitrofen (EXP)

ozone (EXP,ISO)

panobinostat (ISO)

paracetamol (ISO)

permethrin (EXP)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

poly(I:C) (EXP)

propanal (ISO)

rac-lactic acid (ISO)

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

SB 431542 (ISO)

sevoflurane (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

T-2 toxin (EXP)

temozolomide (ISO)

testosterone undecanoate (ISO)

thapsigargin (ISO)

tocopherol (ISO)

trichostatin A (ISO)

triclosan (ISO)

trimellitic anhydride (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

autophagy (ISO,ISS)

calcium ion regulated lysosome exocytosis (ISO)

calcium-ion regulated exocytosis (IBA)

cellular response to calcium ion (IBA)

establishment of vesicle localization (ISO,ISS)

learning (ISO,ISS)

memory (ISO,ISS)

negative regulation of clathrin-coated pit assembly (IMP)

negative regulation of clathrin-dependent endocytosis (IMP)

negative regulation of cytokine production (ISO,ISS)

negative regulation of dopamine secretion (IDA,ISO)

negative regulation of endocytosis (IDA,ISO)

negative regulation of interleukin-6 production (ISO,ISS)

negative regulation of membrane invagination (IMP)

negative regulation of microglial cell activation (ISO,ISS)

negative regulation of phagocytosis (ISO,ISS)

negative regulation of synaptic vesicle endocytosis (IMP)

negative regulation of tumor necrosis factor production (ISO,ISS)

plasma membrane repair (ISO)

positive regulation of protein localization to phagocytic vesicle (ISO)

regulation of calcium ion-dependent exocytosis (IBA)

regulation of defense response to bacterium (ISO)

regulation of dopamine secretion (IBA)

response to wounding (ISO)

vesicle fusion (IBA)

vesicle-mediated transport (IBA)

Cellular Component

axon (IBA,IDA)

cell body (IDA)

clathrin-coated vesicle membrane (IEA)

cytoplasm (ISO)

dendrite (ISO,ISS)

dendritic spine (IDA)

early phagosome (ISO,ISS)

excitatory synapse (IDA)

exocytic vesicle (IBA)

inhibitory synapse (IDA)

integral component of plasma membrane (ISO)

integral component of presynaptic active zone membrane (IDA)

integral component of synaptic vesicle membrane (IDA)

lysosomal membrane (IEA)

lysosome (ISO,ISS)

neuron projection (IDA,ISO)

perikaryon (IEA)

perinuclear region of cytoplasm (IDA)

phagocytic cup (ISO)

phagocytic vesicle (ISO)

plasma membrane (IBA)

postsynapse (IDA)

postsynaptic density (IDA,ISO,ISS)

presynapse (IDA)

presynaptic active zone membrane (IDA)

recycling endosome (ISO,ISS)

recycling endosome membrane (IEA)

Schaffer collateral - CA1 synapse (IDA)

synapse (IBA)

synaptic vesicle (IDA,ISO,ISS)

terminal bouton (IDA)

trans-Golgi network (ISO,ISS)

vesicle (IDA,ISO,ISS)

Molecular Function

beta-tubulin binding (ISO)

calcium ion binding (IDA)

calcium-dependent phospholipid binding (IDA)

clathrin binding (IBA)

identical protein binding (ISO)

phosphatidylserine binding (IBA)

protein binding (IPI,ISO)

SNARE binding (IBA,ISO)

translation initiation factor binding (ISO)

ubiquitin protein ligase 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.	Huynh DP, etal., Hum Mol Genet. 2003 Oct 15;12(20):2587-97. Epub 2003 Aug 12.
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 ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Stucchi R, etal., Cell Rep. 2018 Jul 17;24(3):685-700. doi: 10.1016/j.celrep.2018.06.071.
9.	von Poser C, etal., J Biol Chem 1997 May 30;272(22):14314-9.
10.	Wang C, etal., EMBO Rep. 2016 Jan;17(1):47-63. doi: 10.15252/embr.201540689. Epub 2015 Nov 20.
11.	Wang C, etal., Nat Commun. 2018 Jan 8;9(1):81. doi: 10.1038/s41467-017-02593-y.
12.	Yeo H, etal., Neuroscience. 2012 Dec 6;225:35-43. doi: 10.1016/j.neuroscience.2012.08.062. Epub 2012 Sep 7.

Additional References at PubMed

PMID:11171101	PMID:12477932	PMID:15340165	PMID:22871113	PMID:23303671	PMID:24882364	PMID:25063865	PMID:26450452	PMID:27278822	PMID:28686317	PMID:30808661

Genomics

Comparative Map Data

Syt11
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	174,206,032 - 174,232,540 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	174,206,191 - 174,231,964 (-)	Ensembl
Rnor_6.0	2	188,112,301 - 188,138,180 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	188,112,286 - 188,138,177 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	207,511,186 - 207,537,292 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	180,874,372 - 180,897,792 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	180,823,880 - 180,847,884 (-)	NCBI
Celera	2	168,153,180 - 168,176,598 (-)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI

SYT11
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	155,859,567 - 155,885,199 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	155,859,502 - 155,885,199 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	155,829,358 - 155,854,990 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	154,095,924 - 154,121,470 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	152,642,372 - 152,667,908	NCBI
Celera	1	128,902,166 - 128,927,893 (+)	NCBI
Cytogenetic Map	1	q22	NCBI
HuRef	1	127,190,717 - 127,215,698 (+)	NCBI		HuRef
CHM1_1	1	157,225,282 - 157,251,010 (+)	NCBI		CHM1_1

Syt11
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	88,652,006 - 88,682,466 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	3	88,652,007 - 88,682,471 (-)	Ensembl
GRCm38	3	88,744,699 - 88,775,159 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	88,744,700 - 88,775,164 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	88,548,623 - 88,576,521 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	3	88,831,629 - 88,858,467 (-)	NCBI			mm8
Celera	3	88,789,281 - 88,807,170 (-)	NCBI		Celera
Cytogenetic Map	3	F1	NCBI
cM Map	3	38.96	NCBI

Syt11
(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_004955545	2,054,721 - 2,074,526 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955545	2,054,720 - 2,074,526 (+)	NCBI	ChiLan1.0	ChiLan1.0

SYT11
(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	1	135,026,032 - 135,046,943 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	135,026,032 - 135,046,943 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	131,193,999 - 131,218,752 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SYT11
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	41,910,102 - 41,929,020 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	41,912,920 - 41,929,617 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	41,399,356 - 41,418,052 (-)	NCBI
ROS_Cfam_1.0	7	41,777,012 - 41,795,715 (-)	NCBI
UMICH_Zoey_3.1	7	41,557,540 - 41,576,236 (-)	NCBI
UNSW_CanFamBas_1.0	7	41,611,188 - 41,629,888 (-)	NCBI
UU_Cfam_GSD_1.0	7	41,895,351 - 41,914,056 (-)	NCBI

Syt11
(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	26,092,808 - 26,112,972 (+)	NCBI
SpeTri2.0	NW_004936580	5,123,196 - 5,142,976 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SYT11
(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	94,139,347 - 94,163,050 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	94,139,345 - 94,163,091 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	102,885,467 - 102,906,314 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SYT11
(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	7,993,426 - 8,019,256 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	20	7,992,988 - 8,019,238 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666038	7,299,080 - 7,325,012 (-)	NCBI	Vero_WHO_p1.0

Syt11
(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 1.0	NW_004624885	1,246,768 - 1,266,418 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

BF388304

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	174,221,186 - 174,221,339 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	188,127,456 - 188,127,608	NCBI	Rnor6.0
Rnor_5.0	2	207,526,341 - 207,526,493	UniSTS	Rnor5.0
RGSC_v3.4	2	180,887,068 - 180,887,220	UniSTS	RGSC3.4
Celera	2	168,165,873 - 168,166,025	UniSTS
RH 3.4 Map	2	1152.01	UniSTS
Cytogenetic Map	2	q34	UniSTS

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
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	182042367	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43154682	202446871	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43154682	202446871	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43171017	184114403	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46123260	202447032	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56043031	202447032	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118275	202447032	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118463	226797303	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	74786664	206665859	Rat
61374	Edpm2	Estrogen-dependent pituitary mass QTL 2	4.42	0.86	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	76539322	202447032	Rat
1581569	Uae32	Urinary albumin excretion QTL 32		0.0001	urine protein amount (VT:0005160)	urine albumin excretion rate (CMO:0000757)	2	78665619	219826953	Rat
724534	Uae6	Urinary albumin excretion QTL 6	10		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	2	78665619	249053267	Rat
8662832	Vetf7	Vascular elastic tissue fragility QTL 7	3.5		aorta elastin amount (VT:0003905)	aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)	2	81689826	221035911	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	81754530	222436696	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	81754530	227146641	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	112456140	212696837	Rat
634308	Sach6	Saccharin preference QTL 6	4.9		taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	2	112456140	212696837	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	114837527	185876470	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	114837527	185876470	Rat
1578648	Bss11	Bone structure and strength QTL 11	4.7		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	2	114837527	211674221	Rat
1554319	Bmd2	Bone mineral density QTL 2	13.4	0.0001	lumbar vertebra area (VT:0010570)	lumbar vertebra cross-sectional area (CMO:0001689)	2	114837675	212549332	Rat
6907363	Bp357	Blood pressure QTL 357	4.1	0.002	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	129540907	174540907	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	133914684	202447032	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	2	135552573	202446871	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	136445150	202447032	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	136916935	189599348	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	136916935	213594495	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141194931	223265385	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	141194931	223265385	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	141596551	202447032	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	143157029	210020885	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	143657411	190602963	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	143657411	190602963	Rat
6903312	Bw112	Body weight QTL 112	3.2	0.0013	body mass (VT:0001259)	body weight (CMO:0000012)	2	143657569	184114274	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	144599348	189599348	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147798556	192798556	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	149559561	221167075	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	149559561	249053267	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	150341585	189039377	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	150341684	202446871	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	150540301	202447032	Rat
1354609	Niddm62	Non-insulin dependent diabetes mellitus QTL 62	4.72	0.000006	insulin secretion trait (VT:0003564)	plasma insulin level (CMO:0000342)	2	150540301	202447032	Rat
12879845	Cm89	Cardiac mass QTL 89		0.008	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	152413072	175950118	Rat
12879846	Cm90	Cardiac mass QTL 90		0.011	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	2	152413072	175950118	Rat
12879847	Am4	Aortic mass QTL 4		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	152413072	175950118	Rat
11565180	Kidm56	Kidney mass QTL 56		0.003	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	152413072	175950118	Rat
11565181	Bw176	Body weight QTL 176		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	2	152413072	175950118	Rat
2301415	Cm67	Cardiac mass QTL 67		0.003	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	152413072	175950118	Rat
12879836	Kidm61	Kidney mass QTL 61		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	152413072	185122374	Rat
12879837	Am2	Aortic mass QTL 2		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	152413072	185122374	Rat
12879838	Cm86	Cardiac mass QTL 86		0.002	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	152413072	185122374	Rat
12879839	Cm85	Cardiac mass QTL 85		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	152413072	185122374	Rat
12879840	Bw179	Body weight QTL 179		0.005	body mass (VT:0001259)	body weight (CMO:0000012)	2	152413072	185122374	Rat
1359032	Hrtrt18	Heart rate QTL 18			heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	2	157142078	192625452	Rat
1358900	Bw48	Body weight QTL 48	4.88		body mass (VT:0001259)	body weight (CMO:0000012)	2	157142078	211086598	Rat
8662843	Vetf9	Vascular elastic tissue fragility QTL 9	2.05		thoracic aorta molecular composition trait (VT:0010568)	aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)	2	157142078	226277316	Rat
1302793	Bw16	Body weight QTL 16	5	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	2	157142209	202446871	Rat
7488925	Bp364	Blood pressure QTL 364		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	160564068	205564068	Rat
1358356	Srcrt1	Stress Responsive Cort QTL1	3.66		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	2	161699179	222436696	Rat
7488927	Bp365	Blood pressure QTL 365		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	162765032	207765032	Rat
2306901	Bp337	Blood pressure QTL 337		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	164073756	227146641	Rat
1598838	Bp290	Blood pressure QTL 290	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	166539266	211539266	Rat
1549833	Bp257	Blood pressure QTL 257		0.003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	168354880	185122374	Rat
1331734	Bp204	Blood pressure QTL 204	3.61192		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	168358098	223265385	Rat
2307174	Activ3	Activity QTL 3	4.83	0.000058	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	2	168594495	213594495	Rat
61469	Bp16	Blood pressure QTL 16	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	169745596	214745596	Rat
70162	Bp63	Blood pressure QTL 63	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	169745596	214745596	Rat
61473	Bp19	Blood pressure QTL 19	6.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	172710921	175950118	Rat
631522	Bp74	Blood pressure QTL 74		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	172710921	184114403	Rat
7488904	Bp363	Blood pressure QTL 363		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	172982062	175950118	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	321
Count of miRNA genes:	191
Interacting mature miRNAs:	229
Transcripts:	ENSRNOT00000027474
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			1						74		26
Low	3	43	34	19	19	19	8	11		35	15	11	8
Below cutoff			22	22		22

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031667	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232748	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC097294	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF000423	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF375465	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC094518	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473976	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000027474 ⟹ ENSRNOP00000027474

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	174,206,191 - 174,231,964 (-)	Ensembl
Rnor_6.0 Ensembl	2	188,112,286 - 188,138,177 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000107218 ⟹ ENSRNOP00000091028

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	174,206,191 - 174,223,273 (-)	Ensembl

RefSeq Acc Id:

NM_031667 ⟹ NP_113855

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	174,208,491 - 174,231,911 (-)	NCBI
Rnor_6.0	2	188,114,760 - 188,138,180 (-)	NCBI
Rnor_5.0	2	207,511,186 - 207,537,292 (-)	NCBI
RGSC_v3.4	2	180,874,372 - 180,897,792 (-)	RGD
Celera	2	168,153,180 - 168,176,598 (-)	RGD

Sequence:

show sequence

CTTAGCTCAGAGCATCCCTGGAGCATCTAAGAGAAAAACGCAGCTAGCAACCAAGGATCGTACT
GTCGCAGGAGCAGTCGGCCATGCACCTTCCCCTCCCTTGATCTGGAGGTCTACAGCCGGGGCCT
CGGTACTGATCGAGATTTCCAAAGTTGTCTGACCTCTGCAAAAGTGTTTCTATCAACAGCCTCT
GATTACAACATGGCTGAGATCACAAATATACGCCCCAGCTTTGATGTGTCACCAGTAGCGGCTG
GCCTCATCGGCGCCTCTGTGCTGGTGGTGTGTGTCTCTGTGACTGTCTTTGTGTGGACATGCTG
CCACCAGCAGGCGGAGAAGAAGCACAAGACCCCACCGTACAAGTTTATTCATATGCTGAAAGGC
ATTAGCATCTACCCAGAGACCCTCAGCAACAAGAAGAAAATCATCAAAGTTCGGAGGGACAAAG
ATGGTTCTCATAGGGAAAGTGGACGAGGGAACCTGTTAGTAAATGCGGAGTCTGGCCTGCTGAG
CCATGACAGGGATCCCAGAGGGCCTAGCCCTGCATCTTGTATAGACCAGTTACCCATCAAAAGA
GACTATGGGGAAGAACTGAGGAGCCCCATGACCAGCCTGACCCCCGGTGAAAGCAAGCCCACCT
CCCCATCATCGCCAGAGGAAGATGTGATGCTAGGGTCCCTTACCTTCTCGGTGGACTACAACTT
TCCCAAGAAAGCTCTGGTGGTGACAATCCAAGAGGCGCATGGGCTGCCAGTGATGGATGGCCAG
ACCCAGGGCTCCGATCCCTACATCAAAATGACCATTCTTCCTGACAAGCGGCATCGAGTGAAGA
CCCGGGTGCTTCGCAAGACCCTGGACCCCGTGTTTGATGAGACCTTCACCTTCTACGGCATTCC
CTACAGCCAGCTACAGGACCTGGTGCTGCACTTCCTTGTGCTCAGCTTTGATCGCTTCTCTCGG
GATGACGTCATCGGGGAGGTCATGGTGCCCTTGGCTGGAGTGGACCCCAGCACAGGCAAGGTTC
AGCTGACCAGGGACATCATCAAGAGGAACATTCAGAAGTGCATTAGCAGAGGGGAACTCCAGGT
ATCTCTGTCATACCAGCCCGTCGCACAGAGAATGACAGTGGTGGTCCTCAAAGCCAGACACTTG
CCGAAGATGGATATCACCGGTCTCTCAGATCCTTATGTCAAGGTGAACGTCTACTACGGCAGAA
AACGCATTGCCAAGAAGAAAACTCATGTAAAGAAGTGCACTTTGAACCCCATCTTCAATGAGTC
CTTCATCTATGACATCCCCACCGATCTCCTGCCTGATATCAGCATCGAGTTCCTTGTCATTGAC
TTCGATCGTACTACTAAGAATGAGGTGGTAGGGAGGCTGATCTTGGGGGCACACAGTGTCACAA
CCAGTGGTGCAGAACACTGGAGAGAGGTGTGCGAGAGTCCCCGCAAGCCTGTAGCCAAGTGGCA
CAGTCTGAGCGAGTACTAACCCTGGGGCCAGGCGGGGAGGCACACACGGGGAGAGGTGACAGAG
AAGCTGACTCAAAACCTCATTTTAGTCGTAGAAGATTTCTTACAGAACAAACCACACGAAGAAC
CTCACACTCCACACGGCTGCAGATTGGTTCTTAGCGTGAGGATTGCTTTCTTCTCTGCAAGGCA
CTAGACGATCTTTTGTTTTTTAAAATGAGGGGGGAAGAGAAGGGAAGACCCCAAGTCTATATAT
AACAATGTAACCTTATACTTGCATGTCTAATACAAACAAGAAATTAGCCTAACAATAAAAAAAA
AAAAAAAAAAAAAAAAAAGG

hide sequence

RefSeq Acc Id:

XM_006232748 ⟹ XP_006232810

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	174,206,032 - 174,232,540 (-)	NCBI
Rnor_6.0	2	188,112,301 - 188,138,172 (-)	NCBI
Rnor_5.0	2	207,511,186 - 207,537,292 (-)	NCBI

Sequence:

show sequence

AGAGCATCCCTGGAGCATCTAAGAGAAAAACGCAGCTAGCAACCAAGGATCGTACTGTCGCAGG
AGCAGTCGGCCATGCACCTTCCCCTCCCTTGATCTGGAGGTCTACAGCCGGGGCCTCGGTACTG
ATCGAGATTTCCAAAGTTGTCTGACCTCTGCAAAAGTGTTTCTATCAACAGCCTCTGATTACAA
CATGGCTGAGATCACAAATATACGCCCCAGCTTTGATGTGTCACCAGTAGCGGCTGGCCTCATC
GGCGCCTCTGTGCTGGTGGTGTGTGTCTCTGTGACTGTCTTTGTGTGGACATGCTGCCACCAGC
AGGCGGAGAAGAAGCACAAGACCCCACCGTACAAGTTTATTCATATGCTGAAAGGCATTAGCAT
CTACCCAGAGACCCTCAGCAACAAGAAGAAAATCATCAAAGTTCGGAGGGACAAAGATGGTTCT
CATAGGGAAAGTGGACGAGGGAACCTGTTAGTAAATGCGGAGTCTGGCCTGCTGAGCCATGACA
GGGATCCCAGAGGGCCTAGCCCTGCATCTTGTATAGACCAGTTACCCATCAAAAGAGACTATGG
GGAAGAACTGAGGAGCCCCATGACCAGCCTGACCCCCGGTGAAAGCAAGCCCACCTCCCCATCA
TCGCCAGAGGAAGATGTGATGCTAGGGTCCCTTACCTTCTCGGTGGACTACAACTTTCCCAAGA
AAGCTCTGGTGGTGACAATCCAAGAGGCGCATGGGCTGCCAGTGATGGATGGCCAGACCCAGGG
CTCCGATCCCTACATCAAAATGACCATTCTTCCTGACAAGCGGCATCGAGTGAAGACCCGGGTG
CTTCGCAAGACCCTGGACCCCGTGTTTGATGAGACCTTCACCTTCTACGGCATTCCCTACAGCC
AGCTACAGGACCTGGTGCTGCACTTCCTTGTGCTCAGCTTTGATCGCTTCTCTCGGGATGACGT
CATCGGGGAGGTCATGGTGCCCTTGGCTGGAGTGGACCCCAGCACAGGCAAGGTTCAGCTGACC
AGGGACATCATCAAGAGGAACATTCAGAAGTGCATTAGCAGAGGGGAACTCCAGGTATCTCTGT
CATACCAGCCCGTCGCACAGAGAATGACAGTGGTGGTCCTCAAAGCCAGACACTTGCCGAAGAT
GGATATCACCGGTCTCTCAGGTAATCCTTATGTCAAGGTGAACGTCTACTACGGCAGAAAACGC
ATTGCCAAGAAGAAAACTCATGTAAAGAAGTGCACTTTGAACCCCATCTTCAATGAGTCCTTCA
TCTATGACATCCCCACCGATCTCCTGCCTGATATCAGCATCGAGTTCCTTGTCATTGACTTCGA
TCGTACTACTAAGAATGAGGTGGTAGGGAGGCTGATCTTGGGGGCACACAGTGTCACAACCAGT
GGTGCAGAACACTGGAGAGAGGTGTGCGAGAGTCCCCGCAAGCCTGTAGCCAAGTGGCACAGTC
TGAGCGAGTACTAACCCTGGGGCCAGGCGGGGAGGCACACACGGGGAGAGGTGACAGAGAAGCT
GACTCAAAACCTCATTTTAGTCGTAGAAGATTTCTTACAGAACAAACCACACGAAGAACCTCAC
ACTCCACACGGCTGCAGATTGGTTCTTAGCGTGAGGATTGCTTTCTTCTCTGCAAGGCACTAGA
CGATCTTTTGTTTTTTAAAATGAGGGGGGAAGAGAAGGGAAGACCCCAAGTCTATATATAACAA
TGTAACCTTATACTTGCATGTCTAATACAAACAAGAAATTAGCCTAACAATATCAAGTTGCAGA
TTTTAATCCATGAAAATTGTGTTTTGTGCCGAACTGTATTTGCTGATCCCCTGAAATTGGCCTC
TCTTTATCAGGCTTCTCTGGGTTATTCCAGTTTTCCATCACCGCAGGAGAAAAGTCTGCTCTTG
TAAAGCCCCATGTCCCCATCATCCAGTCCCTTTTGCTGTCACCTCTCACATCTCTGCTCTTTGG
CTGAGTTACAAATCCTGAGGTCTGTAGTAAGTGAGGAAATGAGTGGGGTTTCCAGGAGAAAGAG
TGGTTGAGAATGGGATGTGTGGGTAGTAGGCAGCCAGTGACTAGAGATTCCCCTGATGAGCTCA
GGAGGAGTGGGGCTGGACTTAGGACTCTGATTTCTCCAGAAGGAGCAATGGAGGGTTCACCTAG
AGCGAGGTACCTGTGAACAGTACCAGCGCGTCCTGAAAGCTGCTTGCAGGTCAGGGGACCAGGG
GATGAAATAAGATGTCCATGTGGCCCTCTGTGGTGGGCTCTTCATCAGTGGTCAGCAGTCCCAG
GTTTGTAAGGTTACACTGGCTTTTACTTTTCCAGAACTGTGCCGGGCGCTCAGGCATCTCTTCA
TTATGTAGCCAACACAGGTTGCTTTCTGTTTCCTAAGGAAAACAGGCCTCAGCCCCTGAGCTTT
AGAGTGGTGGCTCTTAAGAAAGCCGAGTGGGGCTGAGTTGTAAGACCGTATGAATGCCTTCCGA
GCTCCACTCTCCTCAGCAGAAGCTCACGGCTGGAGAACTGGGAGTCTCCCCACACAGTGAAGGG
TGGAAACCAAAGTTCCACCATGTCTCTGCCACTGCACCAGACAGTGTAGAGCTTGTGCATCGTC
CTGGAGCCCAGACCCAGGTCTCCACGCGGAGACTTCCAGAGGAAACGAGCGGTGAGCTTGGATG
GGCAGTGCCTATTTTGACAGCCTGAAGAGGACCTCAGTCAAATAAGAGATAGCTTGATCCAGGG
CCTGAACAATTAGCTGTAACTGAAGTGCCCACTTCCCTGAAGGCCATCACTTTCTAGCTTGCTT
CTGAGAAGGGGTGGACAAGCTGACTTTCCATGGAGAGGGTTGGTGACAATGCCTTTGGTGGTTC
CCCTCGTGCTTGTGGATCTGAATCCACTCTGCGCCCCCCCCACCCCACCCCCCAACCTCTCATT
TGATTTTGTTTGCTTGGTTTTGTTCTTTTTCTGCCGACTCTTGGCAAGGCAGAGCAGCCCTGTA
CAGACGGGAAACCCCACTGTACTCTTGCTCCTGTCAGCCCTTAAATCCCATAATCTGACTCAGT
GTCTCACCATCAACTGGGATCGCACCACTAGTCTCCGTCCTTTAACCCATGGAGTGTAAATAGT
GTATCATACGTAGAAGAAAATACTTTTTGTTTTCTAAAAAGGCATTTTGACATAGTTTAACGAA
AACCCGGCAGGAGCATTCTAAGCCCCATTAGGGAAAACGATTGAAACGGTTCCTCTTCGTCGCC
TTAATGTGTAGAGATCAGAAGTCACTGCGCAGGCCCTGTCTCCTTGGGAGAAGGGATGCGAAGT
GACAGGTGGAGCCTGGCCTCTGTCCCGCTGTGTGTGCCTCTGTAGCTCCCCCTGAGAAGTCTGG
GAAACAGCCTCACCATGCTCCTCCTCCTTCCCCGTGCCCCTGCAGCTCGATCCTTTGCATCCTC
TGGGTCTGCGGAGCGCGGGTGCTGGTAGGGGAGCCTGTACTTCCACAGGCTCGGGGCTGCCAAG
AAAAGGCAAAGGGGTGGGCAGTACAGGATCCCTCCCTCCTACCTCAGGCCTGATCCATCATGGA
CTTGGTATCCTAACGCTTCTTAGCGGACTCTGGCTTTCACACATGTTCTTCACAGAGCTCACGG
CTGTGGGCAGAGGCAGAACGCCTCTCCCTGGCCATTGAAAGACAAGAGAGTCACATCCTAGCTT
TTGCACAAGGCTCTTGTGGTTAGGAATAGGTTAGGGAAAGGTCACTCCTGATTTCCCAGCAGCC
AGTCTGTCTGTGGAGATTTCTTGACTCCTTGGGGACTCTGAGAACTGTTCCCAATATCAGAAGT
TCCCTCTTGAGTTCTCCTTCTTTCAGCTCTCGGCATGGCCACAGTGTGCGTCTTGGTGGGCAGT
GCCATGCTGGAGAGCAGATCTCCGTGCTGTGGGGCCCAGGGGGACCTACTTAGGAGGGGATATG
GGAGACTTTATTACTGGTCATAGTGACATTGCCCTCACCACAATCCCTCTCCAAAGTGGTCGTC
TTTCTTTACCTTGTGTCTTCTCTTGTAAAAATAAAACTCAAAAATAAAAGTGTCAAATTAAAAA
GAAAAAAAAATGGAAAAAGCTAACACGAACTGTGTGAAGTTGCATAACGCTGTGACGCTAACCT
GCAATGTGTAATGCTATCTTGTATGTGGACCTTGTCAATGCGCCACACACGTGCAGAATAAAGA
CTGACTCAGACTAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_113855	(Get FASTA)	NCBI Sequence Viewer
	XP_006232810	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB58344	(Get FASTA)	NCBI Sequence Viewer
	AAH94518	(Get FASTA)	NCBI Sequence Viewer
	AAK56960	(Get FASTA)	NCBI Sequence Viewer
	EDM00685	(Get FASTA)	NCBI Sequence Viewer
	O08835	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_113855 ⟸ NM_031667

- UniProtKB:

Q505J5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAEITNIRPSFDVSPVAAGLIGASVLVVCVSVTVFVWTCCHQQAEKKHKTPPYKFIHMLKGISI
YPETLSNKKKIIKVRRDKDGSHRESGRGNLLVNAESGLLSHDRDPRGPSPASCIDQLPIKRDYG
EELRSPMTSLTPGESKPTSPSSPEEDVMLGSLTFSVDYNFPKKALVVTIQEAHGLPVMDGQTQG
SDPYIKMTILPDKRHRVKTRVLRKTLDPVFDETFTFYGIPYSQLQDLVLHFLVLSFDRFSRDDV
IGEVMVPLAGVDPSTGKVQLTRDIIKRNIQKCISRGELQVSLSYQPVAQRMTVVVLKARHLPKM
DITGLSDPYVKVNVYYGRKRIAKKKTHVKKCTLNPIFNESFIYDIPTDLLPDISIEFLVIDFDR
TTKNEVVGRLILGAHSVTTSGAEHWREVCESPRKPVAKWHSLSEY

hide sequence

RefSeq Acc Id:	XP_006232810 ⟸ XM_006232748
- Peptide Label:	isoform X1
- UniProtKB:	O08835 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAEITNIRPSFDVSPVAAGLIGASVLVVCVSVTVFVWTCCHQQAEKKHKTPPYKFIHMLKGISI YPETLSNKKKIIKVRRDKDGSHRESGRGNLLVNAESGLLSHDRDPRGPSPASCIDQLPIKRDYG EELRSPMTSLTPGESKPTSPSSPEEDVMLGSLTFSVDYNFPKKALVVTIQEAHGLPVMDGQTQG SDPYIKMTILPDKRHRVKTRVLRKTLDPVFDETFTFYGIPYSQLQDLVLHFLVLSFDRFSRDDV IGEVMVPLAGVDPSTGKVQLTRDIIKRNIQKCISRGELQVSLSYQPVAQRMTVVVLKARHLPKM DITGLSGNPYVKVNVYYGRKRIAKKKTHVKKCTLNPIFNESFIYDIPTDLLPDISIEFLVIDFD RTTKNEVVGRLILGAHSVTTSGAEHWREVCESPRKPVAKWHSLSEY hide sequence

RefSeq Acc Id:

ENSRNOP00000027474 ⟸ ENSRNOT00000027474

RefSeq Acc Id:

ENSRNOP00000091028 ⟸ ENSRNOT00000107218

Protein Domains

Transcriptome

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

Promoters

RGD ID:

13691451

Promoter ID:

EPDNEW_R1976

Type:

initiation region

Name:

Syt11_1

Description:

synaptotagmin 11

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	2	188,138,200 - 188,138,260	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:62042	AgrOrtholog
Ensembl Genes	ENSRNOG00000020279	Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000027474	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000027474	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7315033	IMAGE-MGC_LOAD
InterPro	C2_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C2_domain_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synaptotagmin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SYT11	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:60568	UniProtKB/TrEMBL
MGC_CLONE	MGC:105395	IMAGE-MGC_LOAD
NCBI Gene	60568	ENTREZGENE
PANTHER	PTHR10024:SF115	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PF00168	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Syt11	PhenoGen
PRINTS	C2DOMAIN	UniProtKB/TrEMBL
	SYNAPTOTAGMN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	PS50004	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	SM00239	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49562	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	O08835	ENTREZGENE
	Q505J5	ENTREZGENE, UniProtKB/TrEMBL
	SYT11_RAT	UniProtKB/Swiss-Prot
UniProt Secondary	Q925B6	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Syt11	synaptotagmin 11	Syt11	synaptotagmin XI	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Syt11	synaptotagmin XI		synaptotagmin 11	Name updated	1299863	APPROVED
2002-06-10	Syt11	synaptotagmin 11			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_domains	has a single transmembrane domain and two cytoplasmic C2-domains	730034
gene_expression	mRNA highly expresed in brain	730034
gene_process	may have calcium-independent function, as calcium-binding site in C2A domain appears to be inactive	730034

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