Syt1 (synaptotagmin 1) - Rat Genome Database

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Gene: Syt1 (synaptotagmin 1) Rattus norvegicus
Analyze
Symbol: Syt1
Name: synaptotagmin 1
RGD ID: 3803
Description: Enables several functions, including calmodulin binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in several processes, including positive regulation of dopamine secretion; regulation of vesicle-mediated transport; and response to calcium ion. Located in several cellular components, including excitatory synapse; hippocampal mossy fiber to CA3 synapse; and secretory vesicle. Is integral component of synaptic vesicle membrane. Biomarker of visual epilepsy. Orthologous to human SYT1 (synaptotagmin 1); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: P65; synaptotagmin I; synaptotagmin-1; sytI
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
mRatBN7.2743,813,204 - 44,358,020 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl743,815,785 - 44,357,803 (-)Ensembl
Rnor_6.0750,084,063 - 50,638,996 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl750,084,060 - 50,638,798 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0750,097,034 - 50,289,950 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4747,243,375 - 47,795,496 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1747,261,066 - 47,815,950 (-)NCBI
Celera740,680,324 - 41,216,966 (-)NCBICelera
RH 3.4 Map7348.01RGD
Cytogenetic Map7q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
calcidiol  (EXP)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
Cuprizon  (EXP)
D-glucose  (EXP)
decabromodiphenyl ether  (EXP)
Deguelin  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
glucose  (EXP)
heroin  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
methotrexate  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
Ptaquiloside  (ISO)
sarin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vorinostat  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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17. GOA data from the GO Consortium
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25. Lai Y and Shin YK, Biochem J. 2012 Apr 1;443(1):223-9. doi: 10.1042/BJ20112044.
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29. Matthew WD, etal., J Cell Biol. 1981 Oct;91(1):257-69.
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31. MGD data from the GO Consortium
32. Mori Y, etal., EMBO J. 2008 Jan 9;27(1):76-87. Epub 2007 Nov 29.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Perin MS, etal., Nature 1990 May 17;345(6272):260-3.
35. RGD automated data pipeline
36. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. RGD automated import pipeline for gene-chemical interactions
38. Sampo B, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3666-71.
39. Schivell AE, etal., J Biol Chem. 1996 Nov 1;271(44):27770-5.
40. Shin OH, etal., Neuron. 2003 Jan 9;37(1):99-108.
41. Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
42. Tang X, etal., Int J Biol Macromol. 2017 Mar;96:736-742. doi: 10.1016/j.ijbiomac.2016.12.074. Epub 2017 Jan 3.
43. Thomas DM, etal., Mol Biol Cell. 1999 Jul;10(7):2285-95.
44. Tocco G, etal., Brain Res Mol Brain Res 1996 Sep 1;40(2):229-39.
45. Tokumaru H, etal., Brain Cell Biol. 2008 Dec;36(5-6):173-89. doi: 10.1007/s11068-008-9032-9. Epub 2009 Jan 9.
46. Tucker WC, etal., J Cell Biol. 2003 Jul 21;162(2):199-209. Epub 2003 Jul 14.
47. van den Bogaart G, etal., J Biol Chem. 2012 May 11;287(20):16447-53. doi: 10.1074/jbc.M112.343418. Epub 2012 Mar 23.
48. Vennekate W, etal., Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):11037-42. doi: 10.1073/pnas.1116326109. Epub 2012 Jun 18.
49. Walther K, etal., EMBO Rep. 2001 Jul;2(7):634-40. Epub 2001 Jul 3.
50. Wang Z and Chapman ER, J Biol Chem. 2010 Oct 1;285(40):30759-66. doi: 10.1074/jbc.M110.137745. Epub 2010 Aug 5.
51. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
52. Willshaw A, etal., FEBS Lett. 2004 Feb 13;559(1-3):13-21.
53. Yoshihara M and Montana ES, Neuroscientist. 2004 Dec;10(6):566-74.
54. Yun HJ, etal., Exp Mol Med. 2013 Aug 16;45:e36. doi: 10.1038/emm.2013.68.
55. Zhang Z, etal., Mol Biol Cell. 2011 Jul 1;22(13):2324-36. doi: 10.1091/mbc.E11-02-0159. Epub 2011 May 5.
56. Zhou Q, etal., Nature. 2015 Sep 3;525(7567):62-7. doi: 10.1038/nature14975. Epub 2015 Aug 17.
57. Zhu D, etal., Biochem Biophys Res Commun. 2007 Oct 5;361(4):922-7. Epub 2007 Jul 25.
Additional References at PubMed
PMID:7553862   PMID:7697723   PMID:7954835   PMID:7993622   PMID:8132583   PMID:8626542   PMID:8889548   PMID:9194562   PMID:9819203   PMID:10715114   PMID:11242035   PMID:11562488  
PMID:11754837   PMID:12145198   PMID:12220627   PMID:12496247   PMID:12645522   PMID:12782290   PMID:12873386   PMID:12963743   PMID:14504267   PMID:14622145   PMID:14709554   PMID:14718921  
PMID:14983047   PMID:15016962   PMID:15044754   PMID:15046725   PMID:15071120   PMID:15082773   PMID:15197251   PMID:15238157   PMID:15350218   PMID:15561725   PMID:15628842   PMID:15774481  
PMID:15866046   PMID:16262243   PMID:16293646   PMID:16407767   PMID:16477143   PMID:16491093   PMID:16612384   PMID:16808897   PMID:16893168   PMID:17183698   PMID:17264148   PMID:17360631  
PMID:17478680   PMID:17913838   PMID:18058942   PMID:18410172   PMID:18468511   PMID:18585366   PMID:18622390   PMID:18703708   PMID:18799625   PMID:18956883   PMID:19302798   PMID:19501597  
PMID:19608642   PMID:19632983   PMID:19723500   PMID:20448186   PMID:20573977   PMID:20735850   PMID:20824061   PMID:20978127   PMID:21040848   PMID:21087613   PMID:21287204   PMID:21307259  
PMID:21320440   PMID:21322640   PMID:21344950   PMID:21456023   PMID:21521611   PMID:21576241   PMID:21610074   PMID:21646859   PMID:21928778   PMID:22008253   PMID:22398727   PMID:22609930  
PMID:22810233   PMID:22871113   PMID:22960622   PMID:23091625   PMID:23300284   PMID:23321072   PMID:23617808   PMID:23665582   PMID:23884218   PMID:23954480   PMID:23999003   PMID:24001110  
PMID:24327345   PMID:24423395   PMID:24472545   PMID:24973220   PMID:25716318   PMID:25716321   PMID:26030874   PMID:26202512   PMID:26389740   PMID:26400647   PMID:26667128   PMID:26792839  
PMID:27001899   PMID:27083046   PMID:27791979   PMID:28111077   PMID:28515322   PMID:28686803   PMID:29115943   PMID:29476059   PMID:30964765   PMID:31160571   PMID:31301806   PMID:31431523  
PMID:31932584   PMID:32024024   PMID:32401194   PMID:32808925   PMID:33160605   PMID:33468652   PMID:33536412  


Genomics

Comparative Map Data
Syt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2743,813,204 - 44,358,020 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl743,815,785 - 44,357,803 (-)Ensembl
Rnor_6.0750,084,063 - 50,638,996 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl750,084,060 - 50,638,798 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0750,097,034 - 50,289,950 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4747,243,375 - 47,795,496 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1747,261,066 - 47,815,950 (-)NCBI
Celera740,680,324 - 41,216,966 (-)NCBICelera
RH 3.4 Map7348.01RGD
Cytogenetic Map7q21NCBI
SYT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1278,863,993 - 79,452,008 (+)EnsemblGRCh38hg38GRCh38
GRCh381278,863,982 - 79,452,008 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371279,257,762 - 79,845,788 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361278,135,414 - 78,368,974 (+)NCBINCBI36hg18NCBI36
Build 341278,113,750 - 78,347,311NCBI
Celera1278,924,230 - 79,512,467 (+)NCBI
Cytogenetic Map12q21.2NCBI
HuRef1276,312,006 - 76,901,927 (+)NCBIHuRef
CHM1_11279,224,059 - 79,812,179 (+)NCBICHM1_1
Syt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910108,333,511 - 108,846,852 (-)NCBIGRCm39mm39
GRCm39 Ensembl10108,333,511 - 108,846,843 (-)Ensembl
GRCm3810108,497,650 - 109,010,980 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10108,497,650 - 109,010,982 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710107,935,305 - 108,447,675 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610107,902,359 - 108,414,729 (-)NCBImm8
Celera10110,439,113 - 110,956,164 (-)NCBICelera
Cytogenetic Map10D1NCBI
cM Map1056.52NCBI
Syt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540517,839,884 - 18,372,566 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540517,840,012 - 18,372,156 (+)NCBIChiLan1.0ChiLan1.0
SYT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11279,240,646 - 79,829,923 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1279,595,704 - 79,829,923 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01276,392,955 - 76,981,800 (+)NCBIMhudiblu_PPA_v0panPan3
SYT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11521,629,061 - 22,042,734 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1521,834,763 - 22,042,732 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1521,934,859 - 22,469,519 (+)NCBI
ROS_Cfam_1.01521,856,608 - 22,392,551 (+)NCBI
UMICH_Zoey_3.11521,446,653 - 21,981,053 (+)NCBI
UNSW_CanFamBas_1.01521,507,116 - 22,042,283 (+)NCBI
UU_Cfam_GSD_1.01521,747,161 - 22,282,182 (+)NCBI
Syt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494538,336,962 - 38,847,320 (-)NCBI
SpeTri2.0NW_00493669865,210 - 575,538 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl5101,871,312 - 102,020,847 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.15101,871,313 - 102,394,310 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25106,815,507 - 107,335,980 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11174,442,890 - 75,032,756 (+)NCBI
ChlSab1.1 Ensembl1174,795,207 - 75,032,915 (+)Ensembl
Vero_WHO_p1.0NW_023666037170,421,409 - 171,012,159 (-)NCBI
Syt1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475018,774,670 - 19,313,932 (-)NCBI

Position Markers
D7Rat106  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,910,536 - 43,910,683 (+)MAPPERmRatBN7.2
Rnor_6.0750,181,371 - 50,181,517NCBIRnor6.0
Rnor_5.0750,191,794 - 50,191,940UniSTSRnor5.0
RGSC_v3.4747,338,134 - 47,338,281RGDRGSC3.4
RGSC_v3.4747,338,135 - 47,338,281UniSTSRGSC3.4
RGSC_v3.1747,358,406 - 47,358,552RGD
Celera740,774,551 - 40,774,698UniSTS
RH 3.4 Map7349.8RGD
RH 3.4 Map7349.8UniSTS
RH 2.0 Map7332.8RGD
SHRSP x BN Map727.21RGD
Cytogenetic Map7q21UniSTS
D7Got157  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2744,108,104 - 44,108,355 (+)MAPPERmRatBN7.2
Rnor_6.0750,382,631 - 50,382,881NCBIRnor6.0
Rnor_5.0750,393,982 - 50,394,232UniSTSRnor5.0
RGSC_v3.4747,540,916 - 47,541,167RGDRGSC3.4
RGSC_v3.4747,540,917 - 47,541,167UniSTSRGSC3.4
RGSC_v3.1747,561,188 - 47,561,438RGD
Celera740,971,474 - 40,971,722UniSTS
RH 3.4 Map7347.9UniSTS
RH 3.4 Map7347.9RGD
RH 2.0 Map7341.3RGD
Cytogenetic Map7q21UniSTS
D37792  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,815,731 - 43,815,891 (+)MAPPERmRatBN7.2
Rnor_6.0750,086,591 - 50,086,750NCBIRnor6.0
Rnor_5.0750,096,981 - 50,097,140UniSTSRnor5.0
RGSC_v3.4747,243,322 - 47,243,481UniSTSRGSC3.4
Celera740,680,271 - 40,680,430UniSTS
Cytogenetic Map7q21UniSTS
AW530700  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2744,089,767 - 44,089,943 (+)MAPPERmRatBN7.2
Rnor_6.0750,364,292 - 50,364,467NCBIRnor6.0
Rnor_5.0750,375,643 - 50,375,818UniSTSRnor5.0
RGSC_v3.4747,522,578 - 47,522,753UniSTSRGSC3.4
Celera740,953,342 - 40,953,517UniSTS
RH 3.4 Map7350.6UniSTS
Cytogenetic Map7q21UniSTS
RH78549  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,813,382 - 43,813,545 (+)MAPPERmRatBN7.2
Rnor_6.0750,084,242 - 50,084,404NCBIRnor6.0
Rnor_5.0750,094,632 - 50,094,794UniSTSRnor5.0
RGSC_v3.4747,240,973 - 47,241,135UniSTSRGSC3.4
Celera740,677,923 - 40,678,085UniSTS
Cytogenetic Map7q21UniSTS
RH94645  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,813,276 - 43,813,458 (+)MAPPERmRatBN7.2
Rnor_6.0750,084,136 - 50,084,317NCBIRnor6.0
Rnor_5.0750,094,526 - 50,094,707UniSTSRnor5.0
RGSC_v3.4747,240,867 - 47,241,048UniSTSRGSC3.4
Celera740,677,817 - 40,677,998UniSTS
RH 3.4 Map7348.01UniSTS
Cytogenetic Map7q21UniSTS
BE107999  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,947,624 - 43,947,774 (+)MAPPERmRatBN7.2
Rnor_6.0750,218,457 - 50,218,606NCBIRnor6.0
Rnor_5.0750,229,566 - 50,229,715UniSTSRnor5.0
RGSC_v3.4747,375,907 - 47,376,056UniSTSRGSC3.4
Celera740,811,608 - 40,811,757UniSTS
RH 3.4 Map7351.92UniSTS
Cytogenetic Map7q21UniSTS
RH137968  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2744,206,754 - 44,206,956 (+)MAPPERmRatBN7.2
Rnor_6.0750,485,630 - 50,485,831NCBIRnor6.0
Rnor_5.0750,496,981 - 50,497,182UniSTSRnor5.0
RGSC_v3.4747,642,642 - 47,642,843UniSTSRGSC3.4
Celera741,066,296 - 41,066,497UniSTS
RH 3.4 Map7348.0UniSTS
Cytogenetic Map7q21UniSTS
RH138239  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2744,323,779 - 44,323,950 (+)MAPPERmRatBN7.2
Rnor_6.0750,603,557 - 50,603,727NCBIRnor6.0
Rnor_5.0750,616,068 - 50,616,238UniSTSRnor5.0
RGSC_v3.4747,762,240 - 47,762,410UniSTSRGSC3.4
Celera741,182,950 - 41,183,120UniSTS
RH 3.4 Map7379.1UniSTS
Cytogenetic Map7q21UniSTS
RH140034  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2743,815,871 - 43,816,058 (+)MAPPERmRatBN7.2
Rnor_6.0750,086,731 - 50,086,917NCBIRnor6.0
Rnor_5.0750,097,121 - 50,097,307UniSTSRnor5.0
RGSC_v3.4747,243,462 - 47,243,648UniSTSRGSC3.4
Celera740,680,411 - 40,680,597UniSTS
RH 3.4 Map7350.91UniSTS
Cytogenetic Map7q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:134
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000048880
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 68 1
Low 3 8 23 9 6 9 2 2 6 25 40 11 2
Below cutoff 35 29 27 13 27 6 7 10 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001033680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA924659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ617622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB615786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB731032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO398869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ181550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000048880   ⟹   ENSRNOP00000049624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl743,815,785 - 44,357,803 (-)Ensembl
Rnor_6.0 Ensembl750,086,644 - 50,638,798 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088950   ⟹   ENSRNOP00000069194
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl743,815,785 - 44,357,803 (-)Ensembl
Rnor_6.0 Ensembl750,084,060 - 50,278,842 (-)Ensembl
RefSeq Acc Id: NM_001033680   ⟹   NP_001028852
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2743,815,785 - 44,357,803 (-)NCBI
Rnor_6.0750,086,644 - 50,638,798 (-)NCBI
Rnor_5.0750,097,034 - 50,289,950 (-)NCBI
RGSC_v3.4747,243,375 - 47,795,496 (-)RGD
Celera740,680,324 - 41,216,966 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765353   ⟹   XP_008763575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2743,813,204 - 44,358,020 (-)NCBI
Rnor_6.0750,084,063 - 50,638,996 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594679   ⟹   XP_017450168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2743,813,204 - 44,358,019 (-)NCBI
Rnor_6.0750,084,063 - 50,638,996 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078497   ⟹   XP_038934425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2743,813,204 - 44,358,019 (-)NCBI
RefSeq Acc Id: XM_039078499   ⟹   XP_038934427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2743,813,204 - 44,007,996 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001028852   ⟸   NM_001033680
- UniProtKB: P21707 (UniProtKB/Swiss-Prot),   Q707P0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763575   ⟸   XM_008765353
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450168   ⟸   XM_017594679
- Peptide Label: isoform X1
- UniProtKB: P21707 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000049624   ⟸   ENSRNOT00000048880
RefSeq Acc Id: ENSRNOP00000069194   ⟸   ENSRNOT00000088950
RefSeq Acc Id: XP_038934425   ⟸   XM_039078497
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934427   ⟸   XM_039078499
- Peptide Label: isoform X3
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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/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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
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)
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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
GK/Ox (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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
LEW/Crl (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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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)
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/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
WKY/NCrl (2019)
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Sequenced By: MCW
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/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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3803 AgrOrtholog
BIND 130539
  130591
  130592
  130593
  130594
  130901
  130902
  130903
Ensembl Genes ENSRNOG00000006426 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000049624 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000069194 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000048880 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000088950 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
InterPro C2_dom UniProtKB/Swiss-Prot
  C2_domain_sf UniProtKB/Swiss-Prot
  Synaptotagmin UniProtKB/Swiss-Prot
  Synaptotagmin1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25716 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25716 ENTREZGENE
PANTHER PTHR10024:SF239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/Swiss-Prot
PhenoGen Syt1 PhenoGen
PRINTS C2DOMAIN UniProtKB/Swiss-Prot
  SYNAPTOTAGMN UniProtKB/Swiss-Prot
PROSITE PS50004 UniProtKB/Swiss-Prot
SMART SM00239 UniProtKB/Swiss-Prot
UniProt P21707 ENTREZGENE
  Q707P0 ENTREZGENE, UniProtKB/TrEMBL
  Q707P1_RAT UniProtKB/TrEMBL
  Q707P2_RAT UniProtKB/TrEMBL
  Q707P4_RAT UniProtKB/TrEMBL
  SYT1_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q3S2E6 UniProtKB/Swiss-Prot
  Q707P5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Syt1  synaptotagmin 1  Syt1  synaptotagmin I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Syt1  synaptotagmin I    synaptotagmin 1  Name updated 1299863 APPROVED
2002-06-10 Syt1  synaptotagmin 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression localized on synaptic vesicles 68912
gene_physical_interaction binds to syntaxin-1 68912
gene_physical_interaction binds calmodulin; binds calcium; binds acidic phospholipids with a specificity similar to protein kinase C 729959
gene_process involved in the fast calcium dependent component of neurotransmitter release 68912
gene_regulation binding to syntaxin-1 is stronger in the presence of calcium 68912