Syt2 (synaptotagmin 2) - Rat Genome Database

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Gene: Syt2 (synaptotagmin 2) Rattus norvegicus
Analyze
Symbol: Syt2
Name: synaptotagmin 2
RGD ID: 3804
Description: Enables calcium-dependent phospholipid binding activity and syntaxin binding activity. Predicted to be involved in several processes, including positive regulation of dendrite extension; regulation of secretion by cell; and synaptic vesicle cycle. Located in terminal bouton. Is integral component of synaptic vesicle membrane. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 7. Orthologous to human SYT2 (synaptotagmin 2); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: RATSYNII; synaptotagmin II; synaptotagmin-2; SYNII; sytII
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SS.SR-(Syt2-D13Mit1)/Jr  
QTLs:   Thym2   Bp159  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21346,088,046 - 46,197,976 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1351,534,025 - 51,578,052 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01351,569,248 - 51,577,824 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01356,621,954 - 56,630,530 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41347,690,518 - 47,699,094 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11347,704,560 - 47,713,137 (+)NCBI
Celera1346,512,022 - 46,520,623 (+)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Berntsson RP, etal., Structure. 2013 Sep 3;21(9):1602-11. doi: 10.1016/j.str.2013.06.026. Epub 2013 Aug 8.
2. Charvin N, etal., EMBO J. 1997 Aug 1;16(15):4591-6.
3. Flister MJ, etal., Hypertension. 2013 Apr;61(4):850-6. doi: 10.1161/HYPERTENSIONAHA.111.01008. Epub 2013 Mar 4.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Geppert M, etal., J Biol Chem 1991 Jul 25;266(21):13548-52.
6. Jin R, etal., Nature. 2006 Dec 21;444(7122):1092-5. Epub 2006 Dec 13.
7. Lee BH, etal., Mol Cell. 2004 Sep 10;15(5):741-51.
8. Li C, etal., Nature 1995 Jun 15;375(6532):594-9.
9. Mahrhold S, etal., FEBS Lett. 2006 Apr 3;580(8):2011-4. Epub 2006 Mar 7.
10. MGD data from the GO Consortium
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. Osborne SL, etal., J Biol Chem. 1999 Jan 1;274(1):59-66.
13. RGD automated data pipeline
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Strotmeier J, etal., FEBS Lett. 2012 Feb 17;586(4):310-3. doi: 10.1016/j.febslet.2011.12.037. Epub 2012 Jan 16.
17. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
18. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
20. Zhang QY, etal., Mamm Genome 1997 Sep;8(9):636-41
Additional References at PubMed
PMID:7961887   PMID:7993622   PMID:8626542   PMID:10715114   PMID:10737807   PMID:12118064   PMID:12860971   PMID:14504267   PMID:14709554   PMID:16116949   PMID:16212888   PMID:17192432  
PMID:19709630   PMID:21456023   PMID:22871113   PMID:23172916   PMID:23999003   PMID:29476059   PMID:31431523  


Genomics

Comparative Map Data
Syt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21346,088,046 - 46,197,976 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1351,534,025 - 51,578,052 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01351,569,248 - 51,577,824 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01356,621,954 - 56,630,530 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41347,690,518 - 47,699,094 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11347,704,560 - 47,713,137 (+)NCBI
Celera1346,512,022 - 46,520,623 (+)NCBICelera
Cytogenetic Map13q13NCBI
SYT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1202,590,596 - 202,710,454 (-)EnsemblGRCh38hg38GRCh38
GRCh381202,590,596 - 202,710,454 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371202,559,724 - 202,679,582 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361200,831,511 - 200,946,168 (-)NCBINCBI36hg18NCBI36
Build 341199,296,544 - 199,411,202NCBI
Celera1175,686,865 - 175,807,438 (-)NCBI
Cytogenetic Map1q32.1NCBI
HuRef1173,725,569 - 173,845,371 (-)NCBIHuRef
CHM1_11203,981,971 - 204,101,776 (-)NCBICHM1_1
Syt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391134,574,272 - 134,680,887 (+)NCBIGRCm39mm39
GRCm39 Ensembl1134,574,415 - 134,690,331 (+)Ensembl
GRCm381134,646,534 - 134,753,149 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,646,677 - 134,762,593 (+)EnsemblGRCm38mm10GRCm38
MGSCv371136,543,258 - 136,645,994 (+)NCBIGRCm37mm9NCBIm37
MGSCv361136,463,092 - 136,565,828 (+)NCBImm8
Celera1137,257,554 - 137,373,520 (+)NCBICelera
Cytogenetic Map1E4NCBI
cM Map158.24NCBI
Syt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540638,643,911 - 38,743,222 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540638,638,192 - 38,743,077 (-)NCBIChiLan1.0ChiLan1.0
SYT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11182,484,225 - 182,605,743 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1182,490,401 - 182,538,123 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01178,187,872 - 178,308,522 (-)NCBIMhudiblu_PPA_v0panPan3
SYT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.17497,387 - 509,338 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl7497,394 - 502,952 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha7478,659 - 557,321 (+)NCBI
ROS_Cfam_1.07433,590 - 512,581 (+)NCBI
UMICH_Zoey_3.17422,285 - 501,206 (+)NCBI
UNSW_CanFamBas_1.07531,125 - 609,898 (+)NCBI
UU_Cfam_GSD_1.07554,413 - 633,358 (+)NCBI
Syt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934472,642,164 - 72,749,746 (+)NCBI
SpeTri2.0NW_0049365671,941,651 - 1,984,422 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1024,638,704 - 24,669,846 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11024,638,645 - 24,727,198 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21029,086,244 - 29,094,379 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12526,702,627 - 26,821,108 (+)NCBI
ChlSab1.1 Ensembl2526,808,007 - 26,817,314 (+)Ensembl
Vero_WHO_p1.0NW_02366605527,480,660 - 27,602,721 (+)NCBI
Syt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248078,103,665 - 8,201,567 (+)NCBI

Position Markers
D13Wox6  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01356,629,542 - 56,629,737NCBIRnor5.0
RGSC_v3.41347,698,107 - 47,698,301RGDRGSC3.4
RGSC_v3.11347,712,150 - 47,712,344RGD
RH 3.4 Map13172.5RGD
RH 2.0 Map13381.3RGD
D13Arb8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21346,192,872 - 46,193,066 (+)MAPPERmRatBN7.2
Rnor_6.01351,576,838 - 51,577,031NCBIRnor6.0
Rnor_5.01356,629,544 - 56,629,737UniSTSRnor5.0
RGSC_v3.41347,698,108 - 47,698,301UniSTSRGSC3.4
Celera1346,519,637 - 46,519,830UniSTS
RH 3.4 Map13172.5UniSTS
SHRSP x BN Map1314.7798UniSTS
SHRSP x BN Map1314.7798RGD
Cytogenetic Map13q13UniSTS
D13Mgh18  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map13193.8UniSTS
RH 3.4 Map13193.8RGD
Cytogenetic Map13q13UniSTS
D13Rjr1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01356,629,544 - 56,629,737UniSTSRnor5.0
RGSC_v3.11347,712,150 - 47,712,344RGD
Celera1346,519,637 - 46,519,830UniSTS
RH 3.4 Map13172.5UniSTS
SHRSP x BN Map1314.7798UniSTS
Cytogenetic Map13q13UniSTS
D19Mgh6  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map13193.8UniSTS
RH 2.0 Map13366.6RGD


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134877665553264877Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879472Bp399Blood pressure QTL 399arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135060922853264877Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat


Related Rat Strains
The following Strains have been annotated to Syt2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:246
Count of miRNA genes:163
Interacting mature miRNAs:180
Transcripts:ENSRNOT00000006637
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 32
Low 42 8 29
Below cutoff 3 15 39 23 19 23 6 7 26 10 11 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006637   ⟹   ENSRNOP00000006637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1351,534,025 - 51,578,052 (+)Ensembl
RefSeq Acc Id: NM_012665   ⟹   NP_036797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21346,185,282 - 46,193,859 (+)NCBI
Rnor_6.01351,569,248 - 51,577,824 (+)NCBI
Rnor_5.01356,621,954 - 56,630,530 (+)NCBI
RGSC_v3.41347,690,518 - 47,699,094 (+)RGD
Celera1346,512,022 - 46,520,623 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090348   ⟹   XP_038946276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21346,151,004 - 46,197,976 (+)NCBI
RefSeq Acc Id: XM_039090349   ⟹   XP_038946277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21346,088,046 - 46,197,976 (+)NCBI
RefSeq Acc Id: XM_039090350   ⟹   XP_038946278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21346,152,068 - 46,197,976 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036797   ⟸   NM_012665
- Sequence:
RefSeq Acc Id: ENSRNOP00000006637   ⟸   ENSRNOT00000006637
RefSeq Acc Id: XP_038946277   ⟸   XM_039090349
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946276   ⟸   XM_039090348
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946278   ⟸   XM_039090350
- Peptide Label: isoform X2
Protein Domains
C2

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)
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)
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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

Database Acc Id Source(s)
AGR Gene RGD:3804 AgrOrtholog
BIND 130562
Ensembl Genes ENSRNOG00000004756 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006637 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006637 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptotagmin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptotagmin1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24805 UniProtKB/Swiss-Prot
NCBI Gene 24805 ENTREZGENE
PANTHER PTHR10024:SF223 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syt2 PhenoGen
PRINTS C2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTOTAGMN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC210189
UniProt G3V6M3_RAT UniProtKB/TrEMBL
  P29101 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-11 Syt2  synaptotagmin 2  Syt2  synaptotagmin II  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Syt2  synaptotagmin II    synaptotagmin 2  Name updated 1299863 APPROVED
2003-04-09 Syt2  synaptotagmin 2      Name updated 629478 APPROVED
2002-06-10 Syt2  synaptotagmin 2      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function binds acidic phospholipids, neurexins, syntaxin, and AP2 61047
gene_process may have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse 61047
gene_product member of a family of calcium sensors regulating neurotransmitter release 61047