Syn1 (synapsin I) - Rat Genome Database

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Gene: Syn1 (synapsin I) Rattus norvegicus
Analyze
Symbol: Syn1
Name: synapsin I
RGD ID: 3797
Description: Enables calcium-dependent protein binding activity. Involved in neuron development and synapse organization. Located in several cellular components, including dendrite; presynaptic active zone; and synaptic vesicle. Is anchored component of synaptic vesicle membrane. Is extrinsic component of synaptic vesicle membrane. Human ortholog(s) of this gene implicated in X-linked epilepsy with variable learning disabilities and behavior disorders and non-syndromic X-linked intellectual disability 50. Orthologous to human SYN1 (synapsin I); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: synapsin 1; synapsin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X1,172,208 - 1,227,400 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX1,172,208 - 1,227,396 (+)Ensembl
Rnor_6.0X1,321,315 - 1,379,202 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX1,321,315 - 1,379,198 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X2,136,336 - 2,194,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X12,512,241 - 12,556,160 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X12,585,157 - 12,585,610 (-)NCBI
CeleraX1,741,094 - 1,795,235 (+)NCBICelera
Cytogenetic MapXq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-Hydroxy-6-(8,11,14-pentadecatrienyl)benzoic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-aminopyridine  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
aluminium sulfate (anhydrous)  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butan-1-ol  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
calcium dichloride  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
citric acid  (EXP)
clofibrate  (ISO)
cocaine  (EXP,ISO)
corticosterone  (ISO)
cyfluthrin  (ISO)
cypermethrin  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP)
dicrotophos  (ISO)
dopamine  (ISO)
doxycycline  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
fucoxanthin  (ISO)
fulvestrant  (ISO)
gamma-tocopherol  (ISO)
genistein  (EXP)
glucose  (ISO)
glutathione  (ISO)
hispidulin  (ISO)
ionomycin  (ISO)
ivermectin  (ISO)
ketamine  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
midazolam  (EXP)
Mipafox  (ISO)
muscimol  (EXP)
N-acetyl-L-cysteine  (ISO)
N-methyl-D-aspartic acid  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nitric oxide  (ISO)
okadaic acid  (ISO)
paracetamol  (EXP,ISO)
paraoxon  (ISO)
paraquat  (EXP)
pentachlorophenol  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phenobarbital  (ISO)
phenytoin  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
potassium chloride  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
resveratrol  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
silver atom  (EXP,ISO)
silver(0)  (EXP,ISO)
sirolimus  (ISO)
succimer  (ISO)
testosterone  (EXP)
thyroxine  (ISO)
tocopherol  (ISO)
trichlorfon  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (EXP)
Typhaneoside  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Molecular profiling of synaptic vesicle docking sites reveals novel proteins but few differences between glutamatergic and GABAergic synapses. Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
2. The rat brain postsynaptic density fraction contains a homolog of the Drosophila discs-large tumor suppressor protein. Cho KO, etal., Neuron 1992 Nov;9(5):929-42.
3. Cognitive impairment in metabolically-obese, normal-weight rats: identification of early biomarkers in peripheral blood mononuclear cells. Cifre M, etal., Mol Neurodegener. 2018 Mar 22;13(1):14. doi: 10.1186/s13024-018-0246-8.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. Alterations in BDNF and synapsin I within the occipital cortex and hippocampus after mild traumatic brain injury in the developing rat: reflections of injury-induced neuroplasticity. Griesbach GS, etal., J Neurotrauma 2002 Jul;19(7):803-14.
7. Synapsins as major neuronal Ca2+/S100A1-interacting proteins. Heierhorst J, etal., Biochem J. 1999 Dec 1;344 Pt 2:577-83.
8. Synapsin I (protein I), a nerve terminal-specific phosphoprotein. III. Its association with synaptic vesicles studied in a highly purified synaptic vesicle preparation. Huttner WB, etal., J Cell Biol. 1983 May;96(5):1374-88.
9. Neuronal nitric-oxide synthase localization mediated by a ternary complex with synapsin and CAPON. Jaffrey SR, etal., Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):3199-204. Epub 2002 Feb 26.
10. Decreased expression of synapse-related genes and loss of synapses in major depressive disorder. Kang HJ, etal., Nat Med. 2012 Aug 12. doi: 10.1038/nm.2886.
11. The TRPM7 ion channel functions in cholinergic synaptic vesicles and affects transmitter release. Krapivinsky G, etal., Neuron. 2006 Nov 9;52(3):485-96.
12. Natural lecithin promotes neural network complexity and activity. Latifi S, etal., Sci Rep. 2016 May 27;6:25777. doi: 10.1038/srep25777.
13. A plethora of presynaptic proteins associated with ATP-storing organelles in cultured astrocytes. Maienschein V, etal., Glia. 1999 May;26(3):233-44.
14. Determination and analysis of the primary structure of the nerve terminal specific phosphoprotein, synapsin I. McCaffery CA and DeGennaro LJ, EMBO J 1986 Dec 1;5(12):3167-73.
15. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
18. Effects of phosphorylation and neuronal activity on the control of synapse formation by synapsin I. Perlini LE, etal., J Cell Sci. 2011 Nov 1;124(Pt 21):3643-53. doi: 10.1242/jcs.086223. Epub 2011 Nov 1.
19. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
21. Synapsin I is phosphorylated at Ser603 by p21-activated kinases (PAKs) in vitro and in PC12 cells stimulated with bradykinin. Sakurada K, etal., J Biol Chem 2002 Nov 22;277(47):45473-9.
22. Synapsins: mosaics of shared and individual domains in a family of synaptic vesicle phosphoproteins. Sudhof TC, etal., Science 1989 Sep 29;245(4925):1474-80.
23. Molecular anatomy of a trafficking organelle. Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
24. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Calsyntenins function as synaptogenic adhesion molecules in concert with neurexins. Um JW, etal., Cell Rep. 2014 Mar 27;6(6):1096-109. doi: 10.1016/j.celrep.2014.02.010. Epub 2014 Mar 6.
26. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
27. DGKiota regulates presynaptic release during mGluR-dependent LTD. Yang J, etal., EMBO J. 2011 Jan 5;30(1):165-80. doi: 10.1038/emboj.2010.286. Epub 2010 Nov 30.
Additional References at PubMed
PMID:7568108   PMID:7777057   PMID:7902212   PMID:8559663   PMID:8794863   PMID:8889548   PMID:9593663   PMID:10358015   PMID:10386995   PMID:12438562   PMID:12691665   PMID:14612614  
PMID:14622577   PMID:14688264   PMID:14736746   PMID:15071120   PMID:15079864   PMID:15246689   PMID:15255972   PMID:15381251   PMID:15479642   PMID:15498890   PMID:15752728   PMID:16025111  
PMID:16093379   PMID:16413126   PMID:16621800   PMID:16818724   PMID:17018287   PMID:17114649   PMID:17610355   PMID:17634366   PMID:18242779   PMID:18519737   PMID:18662330   PMID:18692536  
PMID:18703092   PMID:19082768   PMID:19292454   PMID:19603498   PMID:19629758   PMID:19922412   PMID:20368707   PMID:20530578   PMID:21185848   PMID:21307259   PMID:21700703   PMID:21948316  
PMID:22138356   PMID:22871113   PMID:23715865   PMID:24279756   PMID:24280219   PMID:24312498   PMID:24327345   PMID:24361760   PMID:24912137   PMID:25218493   PMID:26173895   PMID:26923581  
PMID:27759003   PMID:28259758   PMID:29476059   PMID:30964765   PMID:31545395   PMID:32357304   PMID:32580014   PMID:33632727  


Genomics

Comparative Map Data
Syn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X1,172,208 - 1,227,400 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX1,172,208 - 1,227,396 (+)Ensembl
Rnor_6.0X1,321,315 - 1,379,202 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX1,321,315 - 1,379,198 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X2,136,336 - 2,194,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X12,512,241 - 12,556,160 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X12,585,157 - 12,585,610 (-)NCBI
CeleraX1,741,094 - 1,795,235 (+)NCBICelera
Cytogenetic MapXq11NCBI
SYN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X47,571,901 - 47,619,857 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX47,571,901 - 47,619,857 (-)EnsemblGRCh38hg38GRCh38
GRCh37X47,431,300 - 47,479,256 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X47,316,244 - 47,364,200 (-)NCBINCBI36hg18NCBI36
Build 34X47,188,586 - 47,235,511NCBI
CeleraX51,626,557 - 51,674,518 (-)NCBI
Cytogenetic MapXp11.3-p11.23NCBI
HuRefX45,143,520 - 45,192,091 (-)NCBIHuRef
CHM1_1X47,462,402 - 47,510,356 (-)NCBICHM1_1
T2T-CHM13v2.0X46,981,791 - 47,029,757 (-)NCBI
Syn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X20,726,750 - 20,787,157 (-)NCBIGRCm39mm39
GRCm39 EnsemblX20,726,750 - 20,787,243 (-)Ensembl
GRCm38X20,860,511 - 20,920,918 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX20,860,511 - 20,921,004 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X20,437,637 - 20,498,044 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X20,017,470 - 20,077,855 (-)NCBImm8
CeleraX18,991,650 - 19,054,780 (-)NCBICelera
Cytogenetic MapXA1.3NCBI
cM MapX16.37NCBI
Syn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955516460,198 - 521,484 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955516460,258 - 521,484 (+)NCBIChiLan1.0ChiLan1.0
SYN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X47,905,598 - 47,951,786 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X40,007,777 - 40,055,801 (-)NCBIMhudiblu_PPA_v0panPan3
SYN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X41,191,571 - 41,241,557 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX41,191,571 - 41,241,640 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX15,566,597 - 15,616,166 (-)NCBI
ROS_Cfam_1.0X41,325,757 - 41,375,351 (-)NCBI
ROS_Cfam_1.0 EnsemblX41,325,762 - 41,375,291 (-)Ensembl
UMICH_Zoey_3.1X41,313,364 - 41,362,911 (-)NCBI
UNSW_CanFamBas_1.0X41,301,640 - 41,351,196 (-)NCBI
UU_Cfam_GSD_1.0X41,394,278 - 41,443,858 (-)NCBI
Syn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X33,494,248 - 33,546,336 (-)NCBI
SpeTri2.0NW_00493650213,334,998 - 13,387,082 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX42,090,245 - 42,142,224 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X42,090,245 - 42,142,254 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,336,634 - 47,388,655 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103231893
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X44,748,994 - 44,797,053 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX44,750,046 - 44,797,009 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236665661,064 - 38,215 (+)NCBIVero_WHO_p1.0
Syn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624978110,506 - 180,568 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624978110,640 - 179,910 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
DXWox10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X1,170,809 - 1,171,026 (+)MAPPERmRatBN7.2
Rnor_6.0X1,319,917 - 1,320,133NCBIRnor6.0
Rnor_5.0X2,134,938 - 2,135,154UniSTSRnor5.0
RGSC_v3.4X12,581,259 - 12,581,475UniSTSRGSC3.4
CeleraX1,739,696 - 1,739,912UniSTS
Cytogenetic MapXq12UniSTS
DXRat60  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X1,175,351 - 1,175,476 (+)MAPPERmRatBN7.2
Rnor_6.0X1,324,321 - 1,324,443NCBIRnor6.0
Rnor_5.0X2,139,263 - 2,139,385UniSTSRnor5.0
RGSC_v3.4X12,503,600 - 12,503,725RGDRGSC3.4
RGSC_v3.4X12,503,601 - 12,503,725UniSTSRGSC3.4
RGSC_v3.1X12,509,156 - 12,509,281RGD
CeleraX1,744,158 - 1,744,280UniSTS
SHRSP x BN MapX0.08UniSTS
SHRSP x BN MapX0.08RGD
Cytogenetic MapXq12UniSTS
UniSTS:224356  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X1,227,192 - 1,227,306 (+)MAPPERmRatBN7.2
Rnor_6.0X1,378,995 - 1,379,108NCBIRnor6.0
Rnor_5.0X2,194,186 - 2,194,299UniSTSRnor5.0
RGSC_v3.4X12,556,705 - 12,556,818UniSTSRGSC3.4
CeleraX1,795,028 - 1,795,141UniSTS
Cytogenetic MapXq11.1UniSTS
Cytogenetic MapXq12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:77
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000014250
Prediction methods:Microtar, Miranda, Pita, 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 72
Low 3 13 28 12 19 12 2 2 2 27 37 11 2
Below cutoff 30 29 29 29 6 9 8 4 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014250   ⟹   ENSRNOP00000014250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX1,172,208 - 1,227,396 (+)Ensembl
Rnor_6.0 EnsemblX1,321,315 - 1,379,198 (+)Ensembl
RefSeq Acc Id: NM_001110782   ⟹   NP_001104252
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X1,172,208 - 1,227,400 (+)NCBI
Rnor_6.0X1,321,315 - 1,379,202 (+)NCBI
Rnor_5.0X2,136,336 - 2,194,393 (+)NCBI
RGSC_v3.4X12,512,241 - 12,556,160 (+)RGD
CeleraX1,741,094 - 1,795,235 (+)NCBI
Sequence:
RefSeq Acc Id: NM_019133   ⟹   NP_062006
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X1,172,208 - 1,227,400 (+)NCBI
Rnor_6.0X1,321,315 - 1,379,202 (+)NCBI
Rnor_5.0X2,136,336 - 2,194,393 (+)NCBI
RGSC_v3.4X12,512,241 - 12,556,160 (+)RGD
CeleraX1,741,094 - 1,795,235 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062006   ⟸   NM_019133
- Peptide Label: isoform a
- UniProtKB: P09951 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104252   ⟸   NM_001110782
- Peptide Label: isoform b
- UniProtKB: P09951 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014250   ⟸   ENSRNOT00000014250

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P09951-F1-model_v2 AlphaFold P09951 1-704 view protein structure

Transcriptome

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

Promoters
RGD ID:13701689
Promoter ID:EPDNEW_R12213
Type:single initiation site
Name:Syn1_1
Description:synapsin I
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X1,321,284 - 1,321,344EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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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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
BUF/N (2020)
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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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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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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
DA/OlaHsd (2019)
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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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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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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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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/Stm (2019)
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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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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
FXLE16/Stm (2020)
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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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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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 1321530 1321531 A T snv ACI/N (MCW), MR/N (MCW), WN/N (MCW)
X 1321563 1321564 G A snv WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3797 AgrOrtholog
BioCyc Gene G2FUF-3201 BioCyc
Ensembl Genes ENSRNOG00000010365 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014250 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014250 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1490.20 UniProtKB/Swiss-Prot
InterPro ATP_grasp_subdomain_1 UniProtKB/Swiss-Prot
  PreATP-grasp_dom_sf UniProtKB/Swiss-Prot
  SYN1 UniProtKB/Swiss-Prot
  Synapsin UniProtKB/Swiss-Prot
  Synapsin_ATP-bd_dom UniProtKB/Swiss-Prot
  Synapsin_CS UniProtKB/Swiss-Prot
  Synapsin_P_site UniProtKB/Swiss-Prot
  Synapsin_pre-ATP-grasp_dom UniProtKB/Swiss-Prot
KEGG Report rno:24949 UniProtKB/Swiss-Prot
NCBI Gene 24949 ENTREZGENE
PANTHER PTHR10841:SF24 UniProtKB/Swiss-Prot
Pfam Synapsin UniProtKB/Swiss-Prot
  Synapsin_C UniProtKB/Swiss-Prot
  Synapsin_N UniProtKB/Swiss-Prot
PhenoGen Syn1 PhenoGen
PRINTS SYNAPSIN UniProtKB/Swiss-Prot
PROSITE SYNAPSIN_1 UniProtKB/Swiss-Prot
  SYNAPSIN_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52440 UniProtKB/Swiss-Prot
TIGR TC224868
UniProt P09951 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9WUX7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Syn1  synapsin I    synapsin 1  Name updated 1299863 APPROVED
2002-06-10 Syn1  synapsin 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation phosphorylated at Ser603 by bradykinin 730063