Syt6 (synaptotagmin 6) - Rat Genome Database

Name: Syt6
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Syt6 (synaptotagmin 6) Rattus norvegicus

Analyze

Symbol:

Syt6

Name:

synaptotagmin 6

RGD ID:

62012

Description:

Exhibits syntaxin binding activity. Involved in presynaptic dense core vesicle exocytosis. Localizes to glutamatergic synapse and integral component of synaptic membrane. Orthologous to human SYT6 (synaptotagmin 6); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 6-propyl-2-thiouracil; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

MGC116356; synaptotagmin VI; synaptotagmin-6; sytVI

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):	SYT6 (synaptotagmin 6)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Syt6 (synaptotagmin VI)	HGNC	Treefam, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Syt6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SYT6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SYT6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Syt6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SYT6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SYT6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Syt6 (synaptotagmin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Syt6 (synaptotagmin VI)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	SYT6 (synaptotagmin 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	syt6b (synaptotagmin VIb)	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	syt6a (synaptotagmin VIa)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	snt-5	Alliance	DIOPT (OrthoFinder\|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	2	191,093,009 - 191,152,283 (+)	NCBI
Rnor_6.0 Ensembl	2	206,064,179 - 206,127,907 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	206,064,181 - 206,119,034 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	225,492,367 - 225,547,221 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	198,807,340 - 198,862,227 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	198,770,093 - 198,824,981 (+)	NCBI
Celera	2	183,565,789 - 183,620,107 (+)	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

breast ductal carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (ISO)

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

6-propyl-2-thiouracil (EXP)

aflatoxin B2 (ISO)

ammonium chloride (EXP)

androgen antagonist (EXP)

arsenite(3-) (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP)

Butylparaben (EXP)

chlorpyrifos (EXP)

clofibrate (ISO)

dorsomorphin (ISO)

enzacamene (EXP)

ethanol (ISO)

flavonoids (EXP)

folic acid (ISO)

hydralazine (ISO)

methapyrilene (ISO)

N-methyl-4-phenylpyridinium (ISO)

paracetamol (EXP,ISO)

phenylmercury acetate (ISO)

rotenone (ISO)

SB 431542 (ISO)

Testosterone propionate (ISO)

thimerosal (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

acrosomal vesicle exocytosis (ISO)

acrosome reaction (IEA,ISO)

calcium-ion regulated exocytosis (IBA)

cellular response to calcium ion (IBA)

presynaptic dense core vesicle exocytosis (IDA,IMP)

regulation of calcium ion-dependent exocytosis (IBA)

regulation of dopamine secretion (IBA)

vesicle-mediated transport (IBA)

Cellular Component

cytosol (ISO,ISS)

exocytic vesicle (IBA)

extrinsic component of membrane (ISO,ISS)

glutamatergic synapse (IDA,IMP)

integral component of membrane (IEA,ISO,ISS)

integral component of synaptic membrane (EXP,IDA)

perinuclear endoplasmic reticulum (ISO)

plasma membrane (IBA,ISO,ISS)

synaptic vesicle membrane (IEA)

Molecular Function

calcium ion binding (IBA)

calcium-dependent phospholipid binding (IBA,ISO)

calcium-dependent protein binding (ISO)

clathrin binding (IBA,ISO)

identical protein binding (ISO)

phosphatidylserine binding (IBA,ISO)

protein binding (ISO)

protein heterodimerization activity (ISO)

protein homodimerization activity (ISO)

SNARE binding (IBA)

syntaxin binding (IBA,IDA,ISO)

References

References - curated


1.	Butz S, etal., J Biol Chem. 1999 Jun 25;274(26):18290-6.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Li C, etal., Nature 1995 Jun 15;375(6532):594-9.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
10.	Wong YH, etal., Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4475-84. doi: 10.1073/pnas.1511830112. Epub 2015 Jul 27.

Additional References at PubMed

PMID:8626542	PMID:10531343	PMID:10531344	PMID:10556508	PMID:11437455	PMID:12477932	PMID:12860971	PMID:15774481

Genomics

Comparative Map Data

Syt6
(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	191,093,009 - 191,152,283 (+)	NCBI
Rnor_6.0 Ensembl	2	206,064,179 - 206,127,907 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	206,064,181 - 206,119,034 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	225,492,367 - 225,547,221 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	198,807,340 - 198,862,227 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	198,770,093 - 198,824,981 (+)	NCBI
Celera	2	183,565,789 - 183,620,107 (+)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI

SYT6
(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	114,089,291 - 114,153,919 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	1	114,089,291 - 114,153,880 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	114,089,292 - 114,153,869 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	114,631,914 - 114,696,491 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	114,433,437 - 114,497,995 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	114,346,428 - 114,408,514	NCBI
Celera	1	112,861,141 - 112,925,712 (-)	NCBI
Cytogenetic Map	1	p13.2	NCBI
HuRef	1	112,489,973 - 112,554,564 (-)	NCBI		HuRef
CHM1_1	1	114,746,727 - 114,811,584 (-)	NCBI		CHM1_1

Syt6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	103,482,561 - 103,552,883 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	3	103,482,547 - 103,552,885 (+)	Ensembl
GRCm38	3	103,575,245 - 103,645,567 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	103,575,231 - 103,645,569 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	103,379,204 - 103,439,102 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	3	103,704,342 - 103,764,239 (+)	NCBI			mm8
Celera	3	105,781,488 - 105,842,192 (+)	NCBI		Celera
Cytogenetic Map	3	F2.2	NCBI

Syt6
(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_004955435	17,347,011 - 17,405,526 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955435	17,349,971 - 17,405,526 (-)	NCBI	ChiLan1.0	ChiLan1.0

SYT6
(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	123,453,698 - 123,514,804 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	123,452,889 - 123,514,795 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	88,397,809 - 88,467,493 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SYT6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	17	51,864,774 - 51,924,676 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	17	51,859,564 - 51,923,044 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Syt6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936690	2,435,573 - 2,497,332 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SYT6
(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	106,425,692 - 106,486,931 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	106,420,614 - 106,485,468 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	116,560,038 - 116,622,295 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SYT6
(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	20	19,497,218 - 19,561,621 (+)	NCBI
ChlSab1.1 Ensembl	20	19,512,540 - 19,563,038 (+)	Ensembl

Syt6
(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_004624772	9,753,485 - 9,810,815 (-)	NCBI

Position Markers

RH142700

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	206,090,642 - 206,090,813	NCBI	Rnor6.0
Rnor_5.0	2	225,518,828 - 225,518,999	UniSTS	Rnor5.0
RGSC_v3.4	2	198,833,801 - 198,833,972	UniSTS	RGSC3.4
RH 3.4 Map	2	1324.1	UniSTS
Cytogenetic Map	2	q34	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
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	140566078	217498545	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	147522550	217498710	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46537589	217498710	Rat
61458	Bp10	Blood pressure QTL 10	3.42		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	204003742	231132207	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43133606	217498545	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43133606	217498545	Rat
61469	Bp16	Blood pressure QTL 16	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
70162	Bp63	Blood pressure QTL 63	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	149114878	225501939	Rat
1331734	Bp204	Blood pressure QTL 204	3.61192		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	181990297	240020001	Rat
1331745	Bp203	Blood pressure QTL 203	4.377		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	204585642	235290110	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56244671	217498710	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141583337	217498710	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828049	217498710	Rat
1298083	Bp158	Blood pressure QTL 158	2.62		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	204003742	231132207	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147122993	240020001	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	147122993	240020001	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	183984665	228984665	Rat
1581499	Esta2	Estrogen-induced thymic atrophy QTL 2			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	204585642	243689611	Rat
738013	Alc15	Alcohol consumption QTL 15	4.1	0.00022	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	2	199380312	244380312	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	157914409	217498545	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	116075644	228737869	Rat
1302793	Bw16	Body weight QTL 16	5	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	2	169852800	217498545	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	254121739	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	237742948	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	161745602	206745602	Rat
1598838	Bp290	Blood pressure QTL 290	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	181522444	226522444	Rat
2301408	Kidm36	Kidney mass QTL 36		0.002	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	205583921	243562243	Rat
2300189	Bmd48	Bone mineral density QTL 48	5.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	2	194378622	239378622	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	116075644	228737869	Rat
1358356	Srcrt1	Stress Responsive Cort QTL1	3.66		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	2	175403337	239166203	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	118446646	227707979	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	138901276	217498710	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	75687495	221880419	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	158159186	217498710	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	83819608	239166203	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828236	243550655	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	83819608	243901375	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	158159186	217498710	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	142053350	228984665	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	118446793	228582621	Rat
2306901	Bp337	Blood pressure QTL 337		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	177680772	243901375	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1359031	Bp275	Blood pressure QTL 275			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	200453324	236318668	Rat
1359031	Bp275	Blood pressure QTL 275			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	200453324	236318668	Rat
1359032	Hrtrt18	Heart rate QTL 18			heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	2	169852670	207612467	Rat
2293084	Iddm26	Insulin dependent diabetes mellitus QTL 26	2.9		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	188838511	228984665	Rat
61366	Iddm3	Insulin dependent diabetes mellitus QTL 3	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	204585642	249585642	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	78321410	217498710	Rat
61398	Bp50	Blood pressure QTL 50	4.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	204585642	249585642	Rat
61417	Cia10	Collagen induced arthritis QTL 10	3.4		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	2	194998627	239998627	Rat
4889834	Pur24	Proteinuria QTL 24	5.8	0.014	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	2	198704357	217498710	Rat
8694435	Bw166	Body weight QTL 166	14.08	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	2	197253963	242253963	Rat
7488929	Bp366	Blood pressure QTL 366		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	199954569	208081195	Rat
9589044	Scfw1	Subcutaneous fat weight QTL 1	5.8	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	2	197253963	242253963	Rat
8694383	Bw158	Body weight QTL 158	7.69	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	2	197253963	242253963	Rat
7488925	Bp364	Blood pressure QTL 364		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	174160958	219160958	Rat
7488927	Bp365	Blood pressure QTL 365		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	177339806	222339806	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	169852670	243026643	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	83754907	237610852	Rat
8694194	Abfw1	Abdominal fat weight QTL 1	11.7	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	2	197253963	242253963	Rat
10043139	Iddm55	Insulin dependent diabetes mellitus QTL 55	3.1	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	205572952	207612467	Rat
10043139	Iddm55	Insulin dependent diabetes mellitus QTL 55	3.1	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	205572952	207612467	Rat
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	16679272	245624402	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	113
Count of miRNA genes:	93
Interacting mature miRNAs:	100
Transcripts:	ENSRNOT00000025953
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			8		8				52	14	4
Low	2	17	1						22	4	24	11
Below cutoff	1	26	21	17	7	17	8	10		16	11		8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_022191	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005500358	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005500359	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005500360	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC099185	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000077	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U20105	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Y19241	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000025953 ⟹ ENSRNOP00000025953

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	206,064,179 - 206,119,034 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000077739 ⟹ ENSRNOP00000069764

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	206,064,394 - 206,127,907 (+)	Ensembl

RefSeq Acc Id:

NM_022191 ⟹ NP_071527

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,093,009 - 191,152,283 (+)	NCBI
Rnor_6.0	2	206,064,181 - 206,119,034 (+)	NCBI
Rnor_5.0	2	225,492,367 - 225,547,221 (+)	NCBI
RGSC_v3.4	2	198,807,340 - 198,862,227 (+)	RGD
Celera	2	183,565,789 - 183,620,107 (+)	RGD

Sequence:

show sequence

TTGAAAAGAAAGAAAAAAGTGATTTCTATGGAGTTGGGACTTGAAACCCAAGACCTACATACGA
CATGTTAACCAAGAGTTCCCCATTGACCTATATATACCCTAGCTCAAGGAACAGTGGATGAATA
ATAGATATTTGGGGGGACCCTGCGGGGAAGTGATTAAAAGCAGAGCCGAGCCTCAGGGGGCCGC
CGCGGGGAGGGTCTTTTGGGGGCCTCCTTGCCCCGCCCCAGTCCGGCCGCGGCTAGAGTTCGAG
TCACTGCTCCGCAGCCCTGAGGATCCGGGGCATGAGCGGAGTTTGGGGGGCCGGAGGGCCTCGG
TGCCAGGCGGCGCTCGCGGTCCTGGCCTCTCTGTGCCGGGCCCGGCCGCCCCCTCTCGGGCTGG
ACGTGGAGACTTGTCAGAGCTTCGAGCTGCAGCCCCCGGAGCAGAGTCCAAGCGCGGCCGACTC
AGGCACCTCTGTCAGCCTCCTCGCAGTGGTAGTTATTGTGTGTGGTGTGGCCCTGGTGGCAGTT
TTTTTCTTTCTCTTTTGGAAGCTGTGCTGGATGCCCTGGAGGAACAAGGAGGCCTCCAGCCCTT
CTTCTGCTAACCCTGCTTCAGAGATCCTCCAAAGCCCCAGCTCCAGAGGCAACATGGCGGATAA
GCTGAAGGACCCCAGTGCCCTGGGCTTCCTGGAGGCAGCTGTAAAGATCAGCCATACTTCCCCA
GATATCCCAGCCGAGGTGCAGATGTCGGTCAAAGAGCACATTATGCGCCACACCAAACTGCAGC
GACAGACCACAGAGCCAGCGTCGTCTACCAGACACACGTCCTTCAAGCGCCACCTGCCACGGCA
GATGCATGTCTCCAGTGTGGACTACGGCAATGAACTGCCGCCGGCCGCCGCTGAACAGCCCACC
AGTATTGGCCGTATCAAGCCTGAGCTCTACAAGCAGAAGTCAGTGGATGGGGATGAGGCCAAGT
CTGAGGCCGCCAAGAGCTGTGGGAAGATCAACTTCAGCCTCCGCTATGACTATGAGAGTGAGAC
CCTGATTGTACGAATCCTGAAGGCCTTTGACCTCCCTGCCAAGGACTTTTGTGGAAGTTCTGAC
CCTTACGTTAAAATCTACCTCTTGCCTGACCGCAAGTGCAAGCTGCAGACCCGGGTGCACCGCA
AGACGCTGAACCCCACCTTTGATGAGAACTTCCACTTCCCCGTGCCCTATGAGGAGCTGGCTGA
CCGCAAGCTGCATCTCAGTGTCTTTGACTTTGACCGCTTCTCCCGCCATGACATGATTGGCGAG
GTCATCCTGGACAATCTCTTCGAGGCCTCTGACCTGTCCCGGGAGACCTCCATCTGGAAGGACA
TCCAGTACGCTACTAGTGAAAGTGTGGACTTGGGAGAGATCATGTTCTCCCTCTGCTACCTGCC
CACAGCAGGCAGGCTCACCCTCACGGTGATCAAGTGTCGCAATCTCAAAGCAATGGATATCACG
GGCTACTCAGATCCCTACGTCAAAGTGTCCCTACTATGTGATGGGCGGAGACTGAAAAAGAAGA
AAACAACCATAAAAAAGAACACCCTCAACCCTGTCTACAACGAGGCCATCATCTTTGATATCCC
CCCAGAAAACATGGATCAAGTGAGCCTGCTCATCTCCGTTATGGACTATGACAGAGTTGGCCAC
AACGAGATCATAGGAGTGTGTAGAGTGGGGATCAGTGCTGAAGGTCTTGGCAGGGACCACTGGA
ATGAGATGTTGGCATACCCACGAAAGCCCATCGCACACTGGCACTGCTTGGCGGAGGTAAAGAA
ATCCTTCAAAGAGGGAACCCCCCGGTTGTGATTTCATTCACGTGGATGCTGCAAGCGG

hide sequence

RefSeq Acc Id:

XM_039103019 ⟹ XP_038958947

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,094,269 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XM_039103020 ⟹ XP_038958948

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,093,057 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XM_039103021 ⟹ XP_038958949

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,094,269 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XM_039103022 ⟹ XP_038958950

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,093,114 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XM_039103023 ⟹ XP_038958951

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,093,562 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XR_005500358

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,094,272 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XR_005500359

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,094,271 - 191,152,283 (+)	NCBI

RefSeq Acc Id:

XR_005500360

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	191,093,566 - 191,152,283 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_071527	(Get FASTA)	NCBI Sequence Viewer
	XP_038958947	(Get FASTA)	NCBI Sequence Viewer
	XP_038958948	(Get FASTA)	NCBI Sequence Viewer
	XP_038958949	(Get FASTA)	NCBI Sequence Viewer
	XP_038958950	(Get FASTA)	NCBI Sequence Viewer
	XP_038958951	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA87724	(Get FASTA)	NCBI Sequence Viewer
	AAH99185	(Get FASTA)	NCBI Sequence Viewer
	EDL85482	(Get FASTA)	NCBI Sequence Viewer
	EDL85483	(Get FASTA)	NCBI Sequence Viewer
	EDL85484	(Get FASTA)	NCBI Sequence Viewer
	EDL85485	(Get FASTA)	NCBI Sequence Viewer
	Q62746	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_071527 ⟸ NM_022191

- UniProtKB:

Q62746 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSGVWGAGGPRCQAALAVLASLCRARPPPLGLDVETCQSFELQPPEQSPSAADSGTSVSLLAVV
VIVCGVALVAVFFFLFWKLCWMPWRNKEASSPSSANPASEILQSPSSRGNMADKLKDPSALGFL
EAAVKISHTSPDIPAEVQMSVKEHIMRHTKLQRQTTEPASSTRHTSFKRHLPRQMHVSSVDYGN
ELPPAAAEQPTSIGRIKPELYKQKSVDGDEAKSEAAKSCGKINFSLRYDYESETLIVRILKAFD
LPAKDFCGSSDPYVKIYLLPDRKCKLQTRVHRKTLNPTFDENFHFPVPYEELADRKLHLSVFDF
DRFSRHDMIGEVILDNLFEASDLSRETSIWKDIQYATSESVDLGEIMFSLCYLPTAGRLTLTVI
KCRNLKAMDITGYSDPYVKVSLLCDGRRLKKKKTTIKKNTLNPVYNEAIIFDIPPENMDQVSLL
ISVMDYDRVGHNEIIGVCRVGISAEGLGRDHWNEMLAYPRKPIAHWHCLAEVKKSFKEGTPRL

hide sequence

RefSeq Acc Id:

ENSRNOP00000069764 ⟸ ENSRNOT00000077739

RefSeq Acc Id:

ENSRNOP00000025953 ⟸ ENSRNOT00000025953

RefSeq Acc Id:	XP_038958948 ⟸ XM_039103020
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038958950 ⟸ XM_039103022
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038958951 ⟸ XM_039103023
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038958947 ⟸ XM_039103019
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038958949 ⟸ XM_039103021
- Peptide Label:	isoform X3

Protein Domains

Transcriptome

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

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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CSV

TAB

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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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CSV

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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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CSV

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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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CSV

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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:62012	AgrOrtholog
BIND	130563
	130911
	130912
	130913
Ensembl Genes	ENSRNOG00000019163	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000025953	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000069764	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000025953	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000077739	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7383303	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
	SYT6	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:60565	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:116356	IMAGE-MGC_LOAD
NCBI Gene	60565	ENTREZGENE
PANTHER	PTHR10024:SF45	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PF00168	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Syt6	PhenoGen
PRINTS	C2DOMAIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SYNAPTOTAGMN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	PS50004	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	SM00239	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC235357
UniProt	A0A0G2JW68_RAT	UniProtKB/TrEMBL
	Q62746	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q4KLI6	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Syt6	synaptotagmin 6	Syt6	synaptotagmin VI	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Syt6	synaptotagmin VI		synaptotagmin 6	Name updated	1299863	APPROVED
2002-06-10	Syt6	synaptotagmin 6			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	specifically expressed in brain	61762
gene_function	bind clathrin-AP2 with high affinity	61762
gene_process	play a general role in endocytosis	61762

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar