Stxbp1 (syntaxin binding protein 1) - Rat Genome Database

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Gene: Stxbp1 (syntaxin binding protein 1) Rattus norvegicus
Analyze
Symbol: Stxbp1
Name: syntaxin binding protein 1
RGD ID: 3785
Description: Enables several functions, including enzyme binding activity; identical protein binding activity; and syntaxin-1 binding activity. Involved in several processes, including positive regulation of secretion by cell; positive regulation of vesicle docking; and regulation of protein-containing complex assembly. Located in several cellular components, including axon; perinuclear region of cytoplasm; and postsynapse. Part of protein-containing complex. Colocalizes with plasma membrane. Human ortholog(s) of this gene implicated in West syndrome and developmental and epileptic encephalopathy 4. Orthologous to human STXBP1 (syntaxin binding protein 1); PARTICIPATES IN insulin secretion pathway; synaptic vesicle exocytosis - neurotransmitter release pathway; INTERACTS WITH 1,3-dinitrobenzene; 2-ethoxyethanol; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ANC18HA; Munc18-1; n-sec1; nSec1; NSEC1A; p67; protein unc-18 homolog 1; protein unc-18 homolog A; rbSec1; rbSec1A; rbSec1B; Sec1; syntaxin-binding protein 1; unc-18 homolog; unc-18-1; unc-18A; Unc18-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2316,076,725 - 16,138,431 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl316,076,391 - 16,138,369 (-)Ensembl
Rnor_6.0311,823,779 - 11,885,479 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,823,785 - 11,885,417 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0317,160,752 - 17,221,893 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,762,105 - 11,825,531 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1311,658,476 - 11,721,903 (-)NCBI
Celera310,816,317 - 10,877,576 (-)NCBICelera
RH 3.4 Map379.6RGD
Cytogenetic Map3p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetohydrazide  (ISO)
acetylsalicylic acid  (EXP)
aconitine  (EXP)
aflatoxin B2  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
Butylparaben  (EXP)
butyric acid  (EXP)
clozapine  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
DDE  (EXP)
decabromodiphenyl ether  (EXP)
Deguelin  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
fluoxetine  (EXP)
formaldehyde  (EXP)
furan  (EXP)
gamma-tocopherol  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
glycine betaine  (EXP)
heroin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linuron  (EXP)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
orphenadrine  (EXP)
ozone  (EXP)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP)
sunitinib  (ISO)
tetrahydropalmatine  (ISO)
thioacetamide  (EXP)
tocopherol  (ISO)
trichostatin A  (EXP,ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bhaskar K, etal., Neurochem Int. 2004 Jan;44(1):35-44.
2. Bin NR, etal., Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4610-5. doi: 10.1073/pnas.1214887110. Epub 2013 Mar 4.
3. Burkhardt P, etal., EMBO J. 2008 Apr 9;27(7):923-33. doi: 10.1038/emboj.2008.37. Epub 2008 Mar 13.
4. Datta P, etal., Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4400-9. doi: 10.1073/pnas.1510111112. Epub 2015 Jul 27.
5. Dawidowski D and Cafiso DS, Structure. 2016 Mar 1;24(3):392-400. doi: 10.1016/j.str.2016.01.005. Epub 2016 Feb 11.
6. Deak F, etal., J Cell Biol. 2009 Mar 9;184(5):751-64. Epub 2009 Mar 2.
7. Deprez L, etal., Neurology. 2010 Sep 28;75(13):1159-65. doi: 10.1212/WNL.0b013e3181f4d7bf.
8. Dulubova I, etal., Proc Natl Acad Sci U S A 2003 Jan 7;100(1):32-7.
9. Dulubova I, etal., Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2697-702. Epub 2007 Feb 14.
10. Garcia EP, etal., J Cell Biol 1995 Apr;129(1):105-20.
11. Garcia EP, etal., Proc Natl Acad Sci U S A 1994 Mar 15;91(6):2003-7.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Guan R, etal., Biochemistry. 2008 Feb 12;47(6):1474-81. Epub 2008 Jan 18.
14. Hata Y, etal., Nature 1993 Nov 25;366(6453):347-51.
15. Hu SH, etal., Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1040-5. doi: 10.1073/pnas.0914906108. Epub 2010 Dec 30.
16. Huang CC, etal., Traffic. 2011 Oct;12(10):1356-70. doi: 10.1111/j.1600-0854.2011.01237.x. Epub 2011 Jul 20.
17. Kim BU, etal., Mol Cells. 2006 Aug 31;22(1):30-5.
18. Kuster A, etal., J Biol Chem. 2015 Sep 10. pii: jbc.M115.666362.
19. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. Lam PP, etal., Mol Biol Cell. 2007 Jul;18(7):2473-80. Epub 2007 Apr 18.
21. Lee HY, etal., J Biol Chem. 2004 Apr 16;279(16):16339-48. Epub 2004 Jan 26.
22. Matsuo N, etal., J Biol Chem 1997 Jun 27;272(26):16438-44.
23. McMahon HT, etal., Cell 1995 Oct 6;83(1):111-9.
24. MGD data from the GO Consortium
25. Misura KM, etal., Nature. 2000 Mar 23;404(6776):355-62.
26. Murphy S, etal., Clin Proteomics. 2015 Nov 23;12:27. doi: 10.1186/s12014-015-9099-0. eCollection 2015.
27. NCBI rat LocusLink and RefSeq merged data July 26, 2002
28. Okamoto M and Sudhof TC, J Biol Chem 1997 Dec 12;272(50):31459-64.
29. OMIM Disease Annotation Pipeline
30. Parisotto D, etal., J Biol Chem. 2012 Sep 7;287(37):31041-9. doi: 10.1074/jbc.M112.386805. Epub 2012 Jul 18.
31. Parisotto D, etal., J Biol Chem. 2014 Apr 4;289(14):9639-50. doi: 10.1074/jbc.M113.514273. Epub 2014 Feb 14.
32. Perez-Branguli F, etal., Mol Cell Neurosci 2002 Jun;20(2):169-80.
33. Pevsner J, etal., Proc Natl Acad Sci U S A 1994 Feb 15;91(4):1445-9.
34. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
35. RGD automated import pipeline for gene-chemical interactions
36. Saitsu H, etal., Nat Genet. 2008 Jun;40(6):782-8. doi: 10.1038/ng.150. Epub 2008 May 11.
37. Sharma VM, etal., Neurochem Int. 2005 Aug;47(3):225-34.
38. Smyth AM, etal., J Biol Chem. 2010 Dec 3;285(49):38141-8. doi: 10.1074/jbc.M110.164038. Epub 2010 Aug 26.
39. Steiner P, etal., Neuroscience 2002;113(4):893-905.
40. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
41. Toonen RF, etal., J Neurochem. 2005 Jun;93(6):1393-400.
42. Wang Z and Thurmond DC, J Cell Sci. 2009 Apr 1;122(Pt 7):893-903.
43. Weckhuysen S, etal., Epilepsia. 2013 May;54(5):e74-80. doi: 10.1111/epi.12124. Epub 2013 Feb 14.
44. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
45. Worst TJ, etal., J Neurosci Res 2005 May 15;80(4):529-38.
Additional References at PubMed
PMID:7536802   PMID:7768895   PMID:7890599   PMID:8631738   PMID:8996080   PMID:11036064   PMID:11545717   PMID:12058058   PMID:12477932   PMID:12730201   PMID:12773094   PMID:14651853  
PMID:15123626   PMID:15145078   PMID:15175344   PMID:15182301   PMID:15255974   PMID:15489334   PMID:15563604   PMID:17002520   PMID:17027648   PMID:17110441   PMID:17167098   PMID:17218264  
PMID:17293448   PMID:17543282   PMID:17617378   PMID:17634366   PMID:18077557   PMID:18703708   PMID:18829865   PMID:19056867   PMID:19144319   PMID:19344701   PMID:19483085   PMID:19573021  
PMID:19748891   PMID:19812250   PMID:19822743   PMID:21266332   PMID:21390273   PMID:21614099   PMID:21730064   PMID:21900493   PMID:21900502   PMID:22411134   PMID:22658674   PMID:22871113  
PMID:23091057   PMID:23223447   PMID:23258414   PMID:23525015   PMID:23761923   PMID:23821748   PMID:23904609   PMID:23962429   PMID:24835618   PMID:25517944   PMID:25716318   PMID:25716321  
PMID:26264872   PMID:26888187   PMID:27597756   PMID:28477408   PMID:28483813   PMID:28827281   PMID:29476059   PMID:29997244   PMID:30622273   PMID:32643828   PMID:32669573   PMID:33159991  
PMID:33468652  


Genomics

Comparative Map Data
Stxbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2316,076,725 - 16,138,431 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl316,076,391 - 16,138,369 (-)Ensembl
Rnor_6.0311,823,779 - 11,885,479 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,823,785 - 11,885,417 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0317,160,752 - 17,221,893 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,762,105 - 11,825,531 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1311,658,476 - 11,721,903 (-)NCBI
Celera310,816,317 - 10,877,576 (-)NCBICelera
RH 3.4 Map379.6RGD
Cytogenetic Map3p11NCBI
STXBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9127,579,370 - 127,696,027 (+)EnsemblGRCh38hg38GRCh38
GRCh389127,611,912 - 127,696,029 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379130,374,191 - 130,458,308 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369129,414,390 - 129,494,816 (+)NCBINCBI36hg18NCBI36
Build 349127,454,121 - 127,534,549NCBI
Celera9101,025,378 - 101,105,881 (+)NCBI
Cytogenetic Map9q34.11NCBI
HuRef999,990,647 - 100,071,101 (+)NCBIHuRef
CHM1_19130,525,679 - 130,606,190 (+)NCBICHM1_1
Stxbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39232,677,619 - 32,737,249 (-)NCBIGRCm39mm39
GRCm39 Ensembl232,677,614 - 32,737,257 (-)Ensembl
GRCm38232,787,607 - 32,847,237 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl232,787,602 - 32,847,245 (-)EnsemblGRCm38mm10GRCm38
MGSCv37232,643,127 - 32,702,757 (-)NCBIGRCm37mm9NCBIm37
MGSCv36232,609,971 - 32,669,135 (-)NCBImm8
Celera232,494,462 - 32,554,183 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.09NCBI
Stxbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955419963,829 - 1,000,759 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955419963,829 - 1,000,759 (-)NCBIChiLan1.0ChiLan1.0
STXBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19127,434,080 - 127,483,971 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9127,434,080 - 127,486,152 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0998,731,527 - 98,811,608 (+)NCBIMhudiblu_PPA_v0panPan3
STXBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1955,690,939 - 55,768,008 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl955,678,264 - 55,727,680 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha954,884,147 - 54,958,397 (-)NCBI
ROS_Cfam_1.0956,612,796 - 56,687,174 (-)NCBI
UMICH_Zoey_3.1955,372,644 - 55,447,116 (-)NCBI
UNSW_CanFamBas_1.0955,687,749 - 55,761,958 (-)NCBI
UU_Cfam_GSD_1.0955,778,988 - 55,853,304 (-)NCBI
Stxbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947195,532,283 - 195,598,947 (+)NCBI
SpeTri2.0NW_00493648715,300,758 - 15,367,475 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STXBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1268,116,118 - 268,213,921 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11268,116,124 - 268,205,805 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21302,023,293 - 302,098,188 (+)NCBISscrofa10.2Sscrofa10.2susScr3
STXBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11210,440,061 - 10,519,798 (-)NCBI
ChlSab1.1 Ensembl1210,439,801 - 10,519,777 (-)Ensembl
Vero_WHO_p1.0NW_0236660795,699,673 - 5,781,129 (+)NCBI
Stxbp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247607,843,741 - 7,914,444 (-)NCBI

Position Markers
AI326233  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,078,026 - 16,078,111 (+)MAPPERmRatBN7.2
Rnor_6.0311,825,081 - 11,825,165NCBIRnor6.0
Rnor_5.0317,162,051 - 17,162,135UniSTSRnor5.0
RGSC_v3.4311,763,402 - 11,763,486UniSTSRGSC3.4
Celera310,817,614 - 10,817,698UniSTS
Cytogenetic Map3p11UniSTS
D45903  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,076,943 - 16,077,048 (+)MAPPERmRatBN7.2
Rnor_6.0311,823,998 - 11,824,102NCBIRnor6.0
Rnor_5.0317,160,968 - 17,161,072UniSTSRnor5.0
RGSC_v3.4311,762,319 - 11,762,423UniSTSRGSC3.4
Celera310,816,531 - 10,816,635UniSTS
Cytogenetic Map3p11UniSTS
RH132234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,082,121 - 16,082,311 (+)MAPPERmRatBN7.2
Rnor_6.0311,829,176 - 11,829,365NCBIRnor6.0
Rnor_5.0317,166,146 - 17,166,335UniSTSRnor5.0
RGSC_v3.4311,767,497 - 11,767,686UniSTSRGSC3.4
Celera310,821,710 - 10,821,899UniSTS
RH 3.4 Map379.9UniSTS
Cytogenetic Map3p11UniSTS
RH144382  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,080,887 - 16,080,990 (+)MAPPERmRatBN7.2
Rnor_6.0311,827,941 - 11,828,043NCBIRnor6.0
Rnor_5.0317,164,911 - 17,165,013UniSTSRnor5.0
RGSC_v3.4311,766,262 - 11,766,364UniSTSRGSC3.4
Celera310,820,473 - 10,820,575UniSTS
RH 3.4 Map381.7UniSTS
Cytogenetic Map3p11UniSTS
RH139424  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,082,121 - 16,082,290 (+)MAPPERmRatBN7.2
Rnor_6.0311,829,176 - 11,829,344NCBIRnor6.0
Rnor_5.0317,166,146 - 17,166,314UniSTSRnor5.0
RGSC_v3.4311,767,497 - 11,767,665UniSTSRGSC3.4
Celera310,821,710 - 10,821,878UniSTS
RH 3.4 Map372.7UniSTS
Cytogenetic Map3p11UniSTS
Stxbp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2316,077,599 - 16,077,844 (+)MAPPERmRatBN7.2
Rnor_6.0311,824,654 - 11,824,898NCBIRnor6.0
Rnor_5.0317,161,624 - 17,161,868UniSTSRnor5.0
RGSC_v3.4311,762,975 - 11,763,219UniSTSRGSC3.4
Celera310,817,187 - 10,817,431UniSTS
RH 3.4 Map379.6UniSTS
Cytogenetic Map3p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:238
Count of miRNA genes:159
Interacting mature miRNAs:182
Transcripts:ENSRNOT00000021178, ENSRNOT00000021189
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 2 34 10 10 9 10 74 22 38 5
Low 1 9 47 31 10 31 8 11 13 3 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021178   ⟹   ENSRNOP00000021178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl316,076,391 - 16,138,319 (-)Ensembl
Rnor_6.0 Ensembl311,823,785 - 11,885,417 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000021189   ⟹   ENSRNOP00000021189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl316,078,344 - 16,138,369 (-)Ensembl
Rnor_6.0 Ensembl311,830,046 - 11,885,311 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106791   ⟹   ENSRNOP00000091076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl316,076,391 - 16,113,068 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110071   ⟹   ENSRNOP00000089501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl316,082,227 - 16,138,369 (-)Ensembl
RefSeq Acc Id: NM_013038   ⟹   NP_037170
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2316,076,730 - 16,138,369 (-)NCBI
Rnor_6.0311,823,784 - 11,885,417 (-)NCBI
Rnor_5.0317,160,752 - 17,221,893 (-)NCBI
RGSC_v3.4311,762,105 - 11,825,531 (-)RGD
Celera310,816,317 - 10,877,576 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233939   ⟹   XP_006234001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2316,076,725 - 16,138,431 (-)NCBI
Rnor_6.0311,823,779 - 11,885,479 (-)NCBI
Rnor_5.0317,160,752 - 17,221,893 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037170   ⟸   NM_013038
- UniProtKB: P61765 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006234001   ⟸   XM_006233939
- Peptide Label: isoform X1
- UniProtKB: P61765 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021189   ⟸   ENSRNOT00000021189
RefSeq Acc Id: ENSRNOP00000021178   ⟸   ENSRNOT00000021178
RefSeq Acc Id: ENSRNOP00000089501   ⟸   ENSRNOT00000110071
RefSeq Acc Id: ENSRNOP00000091076   ⟸   ENSRNOT00000106791

Transcriptome

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

Promoters
RGD ID:13691996
Promoter ID:EPDNEW_R2521
Type:multiple initiation site
Name:Stxbp1_1
Description:syntaxin binding protein 1
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_6.0311,885,426 - 11,885,486EPDNEW

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)
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/Crl (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
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)
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
LEXF10A/StmMcwi (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
LEXF11/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
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
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)
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
PVG/Seac (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
SBH/Ygl (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: 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)
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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
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)
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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
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)
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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 (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
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 (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)
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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 (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
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:3785 AgrOrtholog
BIND 134444
  134446
  134479
  134480
Ensembl Genes ENSRNOG00000015420 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000021178 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000021189 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021178 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000021189 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.1910 UniProtKB/Swiss-Prot
  3.40.50.2060 UniProtKB/Swiss-Prot
  3.90.830.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7315868 IMAGE-MGC_LOAD
InterPro Sec-1-like_dom1 UniProtKB/Swiss-Prot
  Sec-1-like_dom2 UniProtKB/Swiss-Prot
  Sec-1-like_dom3a UniProtKB/Swiss-Prot
  Sec1-like UniProtKB/Swiss-Prot
  Sec1-like_sf UniProtKB/Swiss-Prot
KEGG Report rno:25558 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105262 IMAGE-MGC_LOAD
NCBI Gene 25558 ENTREZGENE
PANTHER PTHR11679 UniProtKB/Swiss-Prot
Pfam Sec1 UniProtKB/Swiss-Prot
PhenoGen Stxbp1 PhenoGen
PIRSF VPS45_Sec1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56815 UniProtKB/Swiss-Prot
TIGR TC228377
UniProt P61765 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q28208 UniProtKB/Swiss-Prot
  Q62759 UniProtKB/Swiss-Prot
  Q64320 UniProtKB/Swiss-Prot
  Q96TG8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Stxbp1  Syntaxin binding protein 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to cytosol and membranes in neuronal tissues 730116
gene_cellular_localization found along axonal plasmalemma in both soluble and membrane-associated forms 729999
gene_expression expressed in brain but not in non-neuronal tissues 1299067
gene_homology 65% identity to D. melanogaster rop; 59% identity to C. elegans unc-18; 27% identity to S. cerevisiae Sec1p 730116
gene_homology homolog of C. elegans gene unc-18 1299066
gene_physical_interaction binding to syntaxin requires N-terminus of syntaxin; binding to SNAP-25 requires C-terminus 1299066
gene_physical_interaction when created as a GST fusion protein, binds with syntaxin but not with SNAP-25 or synaptobrevin/VAMP 1299067
gene_physical_interaction binds syntaxins 1A and 1B 730238
gene_physical_interaction binds to syntaxin 1a, 2, and 3 fusion proteins but not to syntaxin 4 fusion protein 730116
gene_physical_interaction not part of the synaptic SNARE or syntaxin 1/SNAP-25 complexes in situ; associations with syntaxin may not be stable 729999
gene_process may be essential for synaptic vesicle docking and fusion 730116
gene_process may be essential for synaptic vesicle docking and fusion 1299066
gene_process may modulate formation of SNARE complexes in nerve endings 730238
gene_protein 593 amino acid protein 1299067
gene_transcript mRNA upregulated in frontal cortex of AA rat strain compared to ANA rat strain 1358772
gene_transcript found as two alternatively spliced isoforms rbSec1A and rbSec1B in axon 729999