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: Exhibits calcium-dependent protein binding activity. Involved in neuron development and synapse organization. Localizes to several cellular components, including dendrite; presynaptic active zone; and synaptic vesicle membrane. Orthologous to human SYN1 (synapsin I); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-Tetrachlorodibenzofuran; 4-aminopyridine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: synapsin 1; synapsin-1
Orthologs:
Homo sapiens (human) : SYN1 (synapsin I)  HGNC  Alliance
Mus musculus (house mouse) : Syn1 (synapsin I)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Syn1 (synapsin I)
Pan paniscus (bonobo/pygmy chimpanzee) : SYN1 (synapsin I)
Canis lupus familiaris (dog) : SYN1 (synapsin I)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Syn1 (synapsin I)
Sus scrofa (pig) : SYN1 (synapsin I)
Chlorocebus sabaeus (African green monkey) : SYN1 (synapsin I)
Heterocephalus glaber (naked mole-rat) : Syn1 (synapsin I)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
4-aminopyridine  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (EXP)
aflatoxin B1  (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  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
citric acid  (EXP)
clofibrate  (ISO)
cocaine  (EXP,ISO)
cyfluthrin  (ISO)
cypermethrin  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP)
dicrotophos  (ISO)
dopamine  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
gamma-tocopherol  (ISO)
genistein  (EXP)
glutathione  (ISO)
hispidulin  (ISO)
ionomycin  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
methylmercury chloride  (ISO)
midazolam  (EXP)
Mipafox  (ISO)
muscimol  (EXP)
N-acetyl-L-cysteine  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nitric oxide  (ISO)
okadaic acid  (ISO)
paracetamol  (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)
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)
succimer  (ISO)
thyroxine  (ISO)
tocopherol  (ISO)
trichlorfon  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
1. Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
2. Cho KO, etal., Neuron 1992 Nov;9(5):929-42.
3. Cifre M, etal., Mol Neurodegener. 2018 Mar 22;13(1):14. doi: 10.1186/s13024-018-0246-8.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Griesbach GS, etal., J Neurotrauma 2002 Jul;19(7):803-14.
7. Heierhorst J, etal., Biochem J. 1999 Dec 1;344 Pt 2:577-83.
8. Huttner WB, etal., J Cell Biol. 1983 May;96(5):1374-88.
9. Jaffrey SR, etal., Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):3199-204. Epub 2002 Feb 26.
10. Kang HJ, etal., Nat Med. 2012 Aug 12. doi: 10.1038/nm.2886.
11. Krapivinsky G, etal., Neuron. 2006 Nov 9;52(3):485-96.
12. Latifi S, etal., Sci Rep. 2016 May 27;6:25777. doi: 10.1038/srep25777.
13. Maienschein V, etal., Glia. 1999 May;26(3):233-44.
14. McCaffery CA and DeGennaro LJ, EMBO J 1986 Dec 1;5(12):3167-73.
15. MGD data from the GO Consortium
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline
18. Perlini LE, etal., J Cell Sci. 2011 Nov 1;124(Pt 21):3643-53. doi: 10.1242/jcs.086223. Epub 2011 Nov 1.
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Sakurada K, etal., J Biol Chem 2002 Nov 22;277(47):45473-9.
22. Sudhof TC, etal., Science 1989 Sep 29;245(4925):1474-80.
23. Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
24. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. 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. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
27. 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  


Genomics

Comparative Map Data
Syn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
GRCh38.p13 EnsemblX47,571,901 - 47,619,857 (-)EnsemblGRCh38hg38GRCh38
GRCh38X47,571,901 - 47,619,857 (-)NCBIGRCh38GRCh38hg38GRCh38
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
Syn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X20,726,750 - 20,787,157 (-)NCBI
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
CanFam3.1 EnsemblX41,191,571 - 41,241,640 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X41,191,571 - 41,241,557 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Syn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
SYN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 EnsemblX44,750,046 - 44,797,009 (-)Ensembl
ChlSab1.1X44,748,994 - 44,797,053 (-)NCBI
Syn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624978110,640 - 179,910 (-)NCBI

Position Markers
DXWox10  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
Cytogenetic MapXq12UniSTS
SHRSP x BN MapX0.08RGD
SHRSP x BN MapX0.08UniSTS
UniSTS:224356  
Rat AssemblyChrPosition (strand)SourceJBrowse
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 (Rnor_6.0)
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)X144092703Rat

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

Nucleotide Sequences
RefSeq Transcripts NM_001110782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_019133 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07036739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07036740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07036741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07036742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG378858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO401107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ084192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M27812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M27924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MH119182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X04655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014250   ⟹   ENSRNOP00000014250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
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

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 (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
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
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
UniGene Rn.9923 ENTREZGENE
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