Syn3 (synapsin III) - Rat Genome Database

Name: Syn3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Syn3 (synapsin III) Rattus norvegicus

Analyze

Symbol:

Syn3

Name:

synapsin III

RGD ID:

3799

Description:

Exhibits ATP binding activity. Predicted to be involved in synaptic vesicle clustering. Localizes to extrinsic component of synaptic vesicle membrane. Orthologous to human SYN3 (synapsin III); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

synapsin 3; synapsin-3

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):	SYN3 (synapsin III)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Syn3 (synapsin III)	HGNC	Treefam, OrthoMCL, NCBI, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Syn3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SYN3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SYN3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Syn3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SYN3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SYN3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Syn3 (synapsin III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SYN1 (synapsin I)	HGNC	OrthoDB
Homo sapiens (human):	SYN2 (synapsin II)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	SYN3 (synapsin III)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Syn3 (synapsin III)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Syn	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	snn-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

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	7	16,216,055 - 17,808,790 (+)	NCBI
Rnor_6.0 Ensembl	7	23,403,891 - 23,808,602 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	23,403,896 - 23,808,602 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	23,553,831 - 23,958,150 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	19,544,439 - 19,940,847 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	19,552,680 - 19,953,765 (+)	NCBI
Celera	7	14,630,545 - 15,035,838 (+)	NCBI		Celera
Cytogenetic Map	7	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

arteriovenous malformations of the brain (ISO)

autism spectrum disorder (ISS)

fundus dystrophy (ISO)

Pseudoinflammatory Fundus Dystrophy, Finnish Type (ISO)

Sorsby's fundus dystrophy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

choline (ISO)

cocaine (ISO)

crocidolite asbestos (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

dopamine (ISO)

folic acid (ISO)

L-methionine (ISO)

lead diacetate (ISO)

methapyrilene (ISO)

paraquat (EXP)

potassium dichromate (ISO)

sodium arsenite (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

neurotransmitter secretion (IBA,IEA,TAS)

synaptic vesicle clustering (IEA,ISO)

synaptic vesicle cycle (ISO)

Cellular Component

extrinsic component of synaptic vesicle membrane (EXP,IDA)

glutamatergic synapse (IEA,ISO)

postsynaptic density (IEA,ISO)

synapse (ISO)

synaptic vesicle (IDA)

synaptic vesicle membrane (IBA,IEA,ISO)

Molecular Function

ATP binding (IDA,IEA)

protein binding (IPI)

References

References - curated


1.	Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	Hosaka M and Sudhof TC, J Biol Chem 1998 May 29;273(22):13371-4.
5.	Jaffrey SR, etal., Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):3199-204. Epub 2002 Feb 26.
6.	Kao HT, etal., Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4667-72.
7.	Lam PP, etal., Mol Biol Cell. 2007 Jul;18(7):2473-80. Epub 2007 Apr 18.
8.	MGD data from the GO Consortium
9.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
10.	RGD automated data pipeline
11.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10358015	PMID:12040043	PMID:15071120	PMID:17114649	PMID:25843720

Genomics

Comparative Map Data

Syn3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	16,216,055 - 17,808,790 (+)	NCBI
Rnor_6.0 Ensembl	7	23,403,891 - 23,808,602 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	23,403,896 - 23,808,602 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	23,553,831 - 23,958,150 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	19,544,439 - 19,940,847 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	19,552,680 - 19,953,765 (+)	NCBI
Celera	7	14,630,545 - 15,035,838 (+)	NCBI		Celera
Cytogenetic Map	7	q13	NCBI

SYN3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	22	32,512,552 - 33,058,372 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	22	32,507,820 - 33,058,381 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	22	32,507,820 - 33,058,381 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	22	32,903,807 - 33,454,367 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	31,238,540 - 31,732,683 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	22	31,233,093 - 31,727,237	NCBI
Celera	22	16,710,711 - 17,256,522 (-)	NCBI
Cytogenetic Map	22	q12.3	NCBI
HuRef	22	15,865,721 - 16,411,951 (-)	NCBI		HuRef
CHM1_1	22	32,867,892 - 33,413,788 (-)	NCBI		CHM1_1

Syn3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	85,884,610 - 86,336,730 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	85,890,989 - 86,334,760 (-)	Ensembl
GRCm38	10	86,048,746 - 86,498,926 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	86,055,125 - 86,498,896 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	85,511,491 - 85,961,641 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	85,485,308 - 85,928,638 (-)	NCBI			mm8
Celera	10	88,022,524 - 88,480,347 (-)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI

Syn3
(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_004955405	41,455,465 - 41,762,920 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955405	41,450,081 - 41,762,894 (-)	NCBI	ChiLan1.0	ChiLan1.0

SYN3
(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	22	31,373,466 - 31,920,997 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	22	31,373,604 - 31,866,798 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	22	13,517,932 - 14,069,661 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SYN3
(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	10	30,482,870 - 30,923,257 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	10	30,475,134 - 30,927,758 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Syn3
(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_004936492	6,836,441 - 7,253,867 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SYN3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	12,017,784 - 12,578,953 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	12,017,741 - 12,501,995 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	12,196,607 - 12,291,334 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SYN3
(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	19	15,330,179 - 15,821,965 (-)	NCBI

Syn3
(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_004624750	1,663,309 - 1,976,738 (+)	NCBI

Position Markers

D7Mgh9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,645,249 - 23,645,397	NCBI	Rnor6.0
Rnor_5.0	7	23,795,488 - 23,795,636	UniSTS	Rnor5.0
RGSC_v3.4	7	19,778,187 - 19,778,336	RGD	RGSC3.4
RGSC_v3.4	7	19,778,188 - 19,778,336	UniSTS	RGSC3.4
RGSC_v3.1	7	19,788,447 - 19,788,596	RGD
Celera	7	14,861,467 - 14,861,602	UniSTS
RH 2.0 Map	7	79.3	RGD
Cytogenetic Map	7	q13	UniSTS

D7Rat40

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,783,311 - 23,783,552	NCBI	Rnor6.0
Rnor_5.0	7	23,933,259 - 23,933,500	UniSTS	Rnor5.0
RGSC_v3.4	7	19,915,731 - 19,916,213	RGD	RGSC3.4
RGSC_v3.4	7	19,915,925 - 19,916,166	UniSTS	RGSC3.4
RGSC_v3.1	7	19,928,649 - 19,929,131	RGD
Celera	7	15,011,032 - 15,011,271	UniSTS
RH 2.0 Map	7	78.0	RGD
SHRSP x BN Map	7	6.87	RGD
Cytogenetic Map	7	q13	UniSTS

D7Rat216

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,700,654 - 23,700,867	NCBI	Rnor6.0
Rnor_5.0	7	23,850,893 - 23,851,106	UniSTS	Rnor5.0
RGSC_v3.4	7	19,833,592 - 19,833,806	RGD	RGSC3.4
RGSC_v3.4	7	19,833,593 - 19,833,806	UniSTS	RGSC3.4
RGSC_v3.1	7	19,847,222 - 19,847,649	RGD
Celera	7	14,916,655 - 14,916,868	UniSTS
SHRSP x BN Map	7	6.87	UniSTS
SHRSP x BN Map	7	6.87	RGD
Cytogenetic Map	7	q13	UniSTS

RH128273

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,545,609 - 23,545,825	NCBI	Rnor6.0
Rnor_5.0	7	23,695,848 - 23,696,064	UniSTS	Rnor5.0
RGSC_v3.4	7	19,678,548 - 19,678,764	UniSTS	RGSC3.4
Celera	7	14,762,644 - 14,762,860	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH129267

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,545,644 - 23,545,834	NCBI	Rnor6.0
Rnor_5.0	7	23,695,883 - 23,696,073	UniSTS	Rnor5.0
RGSC_v3.4	7	19,678,583 - 19,678,773	UniSTS	RGSC3.4
Celera	7	14,762,679 - 14,762,869	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH94615

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,546,634 - 23,546,707	NCBI	Rnor6.0
Rnor_5.0	7	23,696,873 - 23,696,946	UniSTS	Rnor5.0
RGSC_v3.4	7	19,679,573 - 19,679,646	UniSTS	RGSC3.4
Celera	7	14,763,669 - 14,763,742	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH143027

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,701,731 - 23,701,920	NCBI	Rnor6.0
Rnor_5.0	7	23,851,970 - 23,852,159	UniSTS	Rnor5.0
RGSC_v3.4	7	19,834,670 - 19,834,859	UniSTS	RGSC3.4
Celera	7	14,917,732 - 14,917,921	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH144261

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,574,271 - 23,574,377	NCBI	Rnor6.0
Rnor_5.0	7	23,724,510 - 23,724,616	UniSTS	Rnor5.0
RGSC_v3.4	7	19,707,210 - 19,707,316	UniSTS	RGSC3.4
Celera	7	14,791,244 - 14,791,350	UniSTS
Cytogenetic Map	7	q13	UniSTS

BI278238

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,545,416 - 23,545,518	NCBI	Rnor6.0
Rnor_5.0	7	23,695,655 - 23,695,757	UniSTS	Rnor5.0
RGSC_v3.4	7	19,678,355 - 19,678,457	UniSTS	RGSC3.4
Celera	7	14,762,451 - 14,762,553	UniSTS
Cytogenetic Map	7	q13	UniSTS

BF400160

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,808,746 - 23,808,845	NCBI	Rnor6.0
Rnor_5.0	7	23,958,294 - 23,958,393	UniSTS	Rnor5.0
RGSC_v3.4	7	19,940,991 - 19,941,090	UniSTS	RGSC3.4
Celera	7	15,035,982 - 15,036,081	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH135110

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,544,717 - 23,544,909	NCBI	Rnor6.0
Rnor_5.0	7	23,694,956 - 23,695,148	UniSTS	Rnor5.0
RGSC_v3.4	7	19,677,656 - 19,677,848	UniSTS	RGSC3.4
Celera	7	14,761,752 - 14,761,944	UniSTS
Cytogenetic Map	7	q13	UniSTS

RH141014

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,543,414 - 23,543,608	NCBI	Rnor6.0
Rnor_5.0	7	23,693,653 - 23,693,847	UniSTS	Rnor5.0
RGSC_v3.4	7	19,676,353 - 19,676,547	UniSTS	RGSC3.4
Celera	7	14,760,452 - 14,760,643	UniSTS
Cytogenetic Map	7	q13	UniSTS

Timp3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,546,244 - 23,546,734	NCBI	Rnor6.0
Rnor_5.0	7	23,696,483 - 23,696,973	UniSTS	Rnor5.0
RGSC_v3.4	7	19,679,183 - 19,679,673	UniSTS	RGSC3.4
Celera	7	14,763,279 - 14,763,769	UniSTS
Cytogenetic Map	7	q13	UniSTS

G45201

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	23,584,311 - 23,584,683	NCBI	Rnor6.0
Rnor_6.0	7	23,584,341 - 23,584,683	NCBI	Rnor6.0
Rnor_5.0	7	23,734,580 - 23,734,922	UniSTS	Rnor5.0
Rnor_5.0	7	23,734,550 - 23,734,922	UniSTS	Rnor5.0
RGSC_v3.4	7	19,717,250 - 19,717,622	UniSTS	RGSC3.4
RGSC_v3.4	7	19,717,280 - 19,717,622	UniSTS	RGSC3.4
Celera	7	14,801,176 - 14,801,548	UniSTS
Celera	7	14,801,206 - 14,801,548	UniSTS
Cytogenetic Map	7	q13	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
2298550	Neuinf6	Neuroinflammation QTL 6	3.3		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	7	1	34147172	Rat
9590142	Scort5	Serum corticosterone level QTL 5	24.4	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	1	34828535	Rat
7411566	Bw136	Body weight QTL 136	10.4	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	1	34828535	Rat
724560	Plsm3	Polydactyly-luxate syndrome (PLS) morphotypes QTL 3		0.0003	tibia length (VT:0004357)	tibia length (CMO:0000450)	7	1	37009673	Rat
2317047	Wbc4	White blood cell count QTL 4		0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	7	1	38119654	Rat
1300176	Hrtrt10	Heart rate QTL 10	3.19		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	7	2653138	32258115	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	2920071	124838025	Rat
61410	Bw19	Body weight QTL 19	6.2	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	7	5911477	50911477	Rat
631503	Bp102	Blood pressure QTL 102	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	5951969	50951969	Rat
10755438	Coatc9	Coat color QTL 9		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	9758045	54758045	Rat
9590102	Sffal5	Serum free fatty acids level QTL 5	8.62	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	7	11647102	56647102	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	12328467	67193263	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	12328467	106995532	Rat
1578652	Bmd15	Bone mineral density QTL 15	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	7	12687850	67801690	Rat
10755440	Coatc10	Coat color QTL 10		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	13952179	58952179	Rat
10059592	Kidm45	Kidney mass QTL 45	3.95	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	14445685	59445685	Rat
1582260	Bw72	Body weight QTL 72	3.2	0.0043	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
1582261	Bw69	Body weight QTL 69	3.2	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
1582262	Bw75	Body weight QTL 75	3	0.0038	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
738033	Anxrr6	Anxiety related response QTL 6	4.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	7	22168412	67168412	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	322
Count of miRNA genes:	199
Interacting mature miRNAs:	233
Transcripts:	ENSRNOT00000037918
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									57
Low	3	35	32	16	18	16	2	3	17	35	41	11	2
Below cutoff		8	25	25	1	25	6	8					6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017109	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078557	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078558	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078559	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC133425	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC136584	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC136645	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF056704	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000181	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000182	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000183	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000184	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000185	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000037918 ⟹ ENSRNOP00000036740

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	23,403,891 - 23,808,602 (+)	Ensembl

RefSeq Acc Id:

NM_017109 ⟹ NP_058805

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	17,376,364 - 17,808,790 (+)	NCBI
Rnor_6.0	7	23,403,896 - 23,808,602 (+)	NCBI
Rnor_5.0	7	23,553,831 - 23,958,150 (+)	NCBI
RGSC_v3.4	7	19,544,439 - 19,940,847 (+)	RGD
Celera	7	14,630,545 - 15,035,838 (+)	RGD

Sequence:

show sequence

GCCAAATCGACTAGGTAAACAGAGTCCTGTGAAGCCCACTTCTGGTGGTGCAGAAGCCCCGGGA
TCCTCTGACCCCAAGCCTCCAGCTTCCTGTAGCTGGCAACCTGCACTTCAAACCTCATCTAGCT
GATTTTGTGTGGAAGGAGGCTTCCCATCCATCGCAGCCATGAACTTCCTCCGGAGGCGGCTGTC
AGACAGCAGCTTTGTGGCCAACCTGCCCAATGGCTACATGCCGGACCTGCAGCGCCCAGAGAGC
TCCAGTAGCTCCCCAGCATCCCCAGCCACAGAGAGAAGGCATCCCCAGCCCCTGGCTGCCTCCT
TCTCTTCTCCAGGATCCAGCCTGTTTAGCTCCTTCTCCAGTGCCATGAAACAGACCCCACAGGC
CCCGACAGGGCTAATGGAACCACCAACTCCTGTCACACCTGTGGTTCAAAGACCCAGGATCTTG
TTGGTCATTGATGATGCCCACACAGACTGGTCGAAATATTTTCATGGGAAGAAAGTGAATGGCG
ACATTGAGATCCGGGTGGAACAGGCTGAGTTCTCTGAGCTGAACCTGGCTGCTTATGTCACCGG
AGGCTGCATGGTGGACATGCAAGTTGTGAGAAATGGCACCAAAATTGTGCGGTCCTTCAAACCT
GACTTCATTCTGGTTAGACAGCATGCCTATAGCATGGCCCTGGCTGAGGACTACCGAAGCCTGG
TCATCGGCCTCCAGTATGGAGGGCTTCCTGCTGTCAACTCTCTCTACTCCGTATACAACTTCTG
CAGCAAGCCTTGGGTGTTCTCTCAGCTCATTAAGATCTTCCATTCCTTGGGTCCTGAGAAGTTT
CCACTAGTGGAGCAAACATTTTTCCCCAACCACAAGCCAATGCTCACAGCCCCGAACTTCCCTG
TGGTGATCAAGCTGGGACACGCTCATGCTGGCATGGGAAAGATCAAAGTAGAAAACCAGCACGA
CTACCAGGACATCACCAGCGTGGTGGCCATGGCCAAAACCTATGCCACCACGGAGGCCTTTATT
GACTCCAAGTATGACATCCGCATACAGAAGATCGGATCCAACTACAAGGCATACATGAGAACCT
CCATCTCTGGAAACTGGAAGGCCAACACAGGCTCTGCTATGCTGGAGCAGGTGGCCATGACGGA
AAGGTACAGGCTGTGGGTGGACAGCTGCTCAGAAATGTTCGGCGGCCTAGACATCTGTGCTGTC
AAGGCCGTTCACAGCAAGAATGGCAGAGATTATATCATTGAGGTCATGGACAGTTCAATGCCAC
TGATTGGAGAACATGTGGAGGAGGACAAGCAGTTAATGGCTGACCTTGTTGTTTCCAAGATGAG
CCAACTCCTGGTGCCAGGGGCCTCGGTGCCCTCCCCCCTGAGACCTTGGGGTCCACAGACTAAA
TCTGCAAAATCTCCAGGGCAAGGCCAGCTAGGACCTCTGCTCGGACAGCCCCAGCCAAGGCCAC
CTCCACAAGGGGGCCCTCGTCAGGCTCAGTCTCCTCAGCCTCCCAGATCTAGAAGTCCATCCCA
GCAGAGGCTCTCCCCACAAGGTCAGCAGCCTGTGAGTCCCCAGTCAGGATCCCCACAGCAGCAA
AGGTCACCAGGTTCTCCACAGCTATCCCGGGCATCTGGCGGCAGTTCTCCAAACCAGGCCTCCA
AGCCAACTGCCAGTCTCAGTTCACATACCCGGCCTCCTGTGCAGGGACGCAGCACCTCCCAGCA
GGGTGAAGAACCCCAAAAGACAGCATCACCTCACCCCCACCTCAACAAATCTCAGTCCCTGACT
AACAGCCTCAGCACGTCAGATACCTCCCATCGAGGAACCCCAAGTGAAGATGAGGCCAAGGCTG
AGACAATCCGCAACCTGAGGAAGTCCTTTGCCAGCCTCTTCTCCGACTAGCCTCTATCCAGGCT
GGAGGACAGGAGGGCAAGAAGACTCAGTGACTGGAGCCCTGTCTGGTTCCCTCCTTCTCAGCCT
TGGTTCCTGATGGAAATATGCTTCCTAAATACATCTGTCCCAGGAACTGGTGATCTACATTCCC
ACCTCCTTGACCATGACATTCTAATGCTGTCTGACTGAGCGGTAGCCTTGAGAGCCCCTAGGTT
CCTCAACACGGACCTTCTAGACAGACAAGGCATCACTACATCCACCATACGCTTGCTCCCTGCC
GCCGGTACCACGTGAGATGTCTGTGTGGCTTGTTTTTGCAGTCTTATTAGTATTTTGCTTGCCT
TTGGGCTGAGGCCCCCTTCTAAGCTGTGAC

hide sequence

RefSeq Acc Id:

XM_039078556 ⟹ XP_038934484

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	16,216,058 - 17,808,790 (+)	NCBI

RefSeq Acc Id:

XM_039078557 ⟹ XP_038934485

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	16,955,344 - 17,802,580 (+)	NCBI

RefSeq Acc Id:

XM_039078558 ⟹ XP_038934486

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	16,216,078 - 17,807,632 (+)	NCBI

RefSeq Acc Id:

XM_039078559 ⟹ XP_038934487

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	16,216,055 - 17,802,580 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_058805	(Get FASTA)	NCBI Sequence Viewer
	XP_038934484	(Get FASTA)	NCBI Sequence Viewer
	XP_038934485	(Get FASTA)	NCBI Sequence Viewer
	XP_038934486	(Get FASTA)	NCBI Sequence Viewer
	XP_038934487	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC24521	(Get FASTA)	NCBI Sequence Viewer
	EDM17123	(Get FASTA)	NCBI Sequence Viewer
	EDM17124	(Get FASTA)	NCBI Sequence Viewer
	O70441	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_058805 ⟸ NM_017109

- UniProtKB:

O70441 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MNFLRRRLSDSSFVANLPNGYMPDLQRPESSSSSPASPATERRHPQPLAASFSSPGSSLFSSFS
SAMKQTPQAPTGLMEPPTPVTPVVQRPRILLVIDDAHTDWSKYFHGKKVNGDIEIRVEQAEFSE
LNLAAYVTGGCMVDMQVVRNGTKIVRSFKPDFILVRQHAYSMALAEDYRSLVIGLQYGGLPAVN
SLYSVYNFCSKPWVFSQLIKIFHSLGPEKFPLVEQTFFPNHKPMLTAPNFPVVIKLGHAHAGMG
KIKVENQHDYQDITSVVAMAKTYATTEAFIDSKYDIRIQKIGSNYKAYMRTSISGNWKANTGSA
MLEQVAMTERYRLWVDSCSEMFGGLDICAVKAVHSKNGRDYIIEVMDSSMPLIGEHVEEDKQLM
ADLVVSKMSQLLVPGASVPSPLRPWGPQTKSAKSPGQGQLGPLLGQPQPRPPPQGGPRQAQSPQ
PPRSRSPSQQRLSPQGQQPVSPQSGSPQQQRSPGSPQLSRASGGSSPNQASKPTASLSSHTRPP
VQGRSTSQQGEEPQKTASPHPHLNKSQSLTNSLSTSDTSHRGTPSEDEAKAETIRNLRKSFASL
FSD

hide sequence

RefSeq Acc Id:

ENSRNOP00000036740 ⟸ ENSRNOT00000037918

RefSeq Acc Id:	XP_038934487 ⟸ XM_039078559
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038934484 ⟸ XM_039078556
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038934486 ⟸ XM_039078558
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038934485 ⟸ XM_039078557
- Peptide Label:	isoform X1

Protein Domains

Synapsin Synapsin_C

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3799	AgrOrtholog
Ensembl Genes	ENSRNOG00000026866	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000036740	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000037918	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.1490.20	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	ATP_grasp_subdomain_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PreATP-grasp_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SYN2/3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_ATP-bd_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_P_site	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_pre-ATP-grasp_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:29130	UniProtKB/Swiss-Prot
NCBI Gene	29130	ENTREZGENE
PANTHER	PTHR10841:SF20	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Synapsin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Synapsin_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Syn3	PhenoGen
PRINTS	SYNAPSIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	SYNAPSIN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SYNAPSIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF52440	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A096MIT7_RAT	UniProtKB/TrEMBL
	O70441	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Syn3	synapsin III		synapsin 3	Name updated	1299863	APPROVED
2002-06-10	Syn3	synapsin 3			Name updated	70585	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_function	binds ATP with high affinity and ADP with a lower affinity	70029
gene_regulation	ATP binding is inhibited by Ca2+	70029

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

Imported Disease Annotations - MGI