Snap25 (synaptosome associated protein 25) - Rat Genome Database
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Gene: Snap25 (synaptosome associated protein 25) Rattus norvegicus
Analyze
Symbol: Snap25
Name: synaptosome associated protein 25
RGD ID: 3728
Description: Exhibits several functions, including calcium-dependent protein binding activity; ion channel binding activity; and syntaxin-1 binding activity. Involved in several processes, including SNARE complex assembly; regulation of nervous system development; and signal release. Localizes to several cellular components, including presynaptic membrane; synaptobrevin 2-SNAP-25-syntaxin-1a complex; and synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex. Predicted to colocalize with BLOC-1 complex and vesicle. Human ortholog(s) of this gene implicated in Down syndrome and congenital myasthenic syndrome 18. Orthologous to human SNAP25 (synaptosome associated protein 25); PARTICIPATES IN insulin secretion pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,2',4,4'-Tetrabromodiphenyl ether; 3,3',5,5'-tetrabromobisphenol A.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: MGC105414; SNAP-25; SNAP-25a; SNAP-25B; SUP; super protein; Synaptosomal-accosiated protein, 25 kDa; synaptosomal-associated 25 kDa protein; synaptosomal-associated protein; synaptosomal-associated protein 25; Synaptosomal-associated protein 25 kDa; synaptosomal-associated protein, 25 kDa
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03129,697,408 - 129,788,417 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3129,599,353 - 129,788,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03136,182,051 - 136,269,422 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43124,806,637 - 124,894,653 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13124,712,177 - 124,800,221 (+)NCBI
Celera3122,761,455 - 122,842,679 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2,2-tetramine  (ISO)
2-methylcholine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
6-propyl-2-thiouracil  (EXP)
8-(4-chlorophenylthio)-cAMP  (EXP)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (EXP)
atrazine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
bicalutamide  (ISO)
bisphenol A  (EXP,ISO)
Botulinum toxin type A  (EXP,ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
cisplatin  (EXP,ISO)
clozapine  (EXP,ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
D-glucose  (EXP)
DDE  (EXP)
decabromodiphenyl ether  (EXP)
dichlorine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
ethanol  (EXP)
fisetin  (ISO)
flavonoids  (EXP)
glucose  (EXP)
haloperidol  (EXP,ISO)
heroin  (ISO)
hydrazines  (ISO)
hydrogen peroxide  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methylamine  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
methylseleninic acid  (ISO)
minocycline  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
Nonylphenol  (EXP)
olanzapine  (ISO)
ozone  (EXP)
panobinostat  (ISO)
PCB138  (EXP)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
potassium chloride  (EXP)
potassium dichromate  (ISO)
pravastatin  (ISO)
propofol  (EXP)
risperidone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
thalidomide  (EXP)
thimerosal  (EXP)
trichostatin A  (EXP,ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aikawa Y, etal., Mol Biol Cell. 2006 May;17(5):2113-24. Epub 2006 Feb 15.
2. Bar-On D, etal., FEBS Lett. 2008 Oct 15;582(23-24):3563-8. doi: 10.1016/j.febslet.2008.08.040. Epub 2008 Sep 24.
3. Basheer R, etal., J Neurosci Res. 2005 Dec 1;82(5):650-8.
4. Bethani I, etal., EMBO J. 2007 Sep 5;26(17):3981-92. Epub 2007 Aug 23.
5. Blasi J, etal., Nature. 1993 Sep 9;365(6442):160-3. doi: 10.1038/365160a0.
6. Burkhardt P, etal., EMBO J. 2008 Apr 9;27(7):923-33. doi: 10.1038/emboj.2008.37. Epub 2008 Mar 13.
7. Chang LF, etal., Nat Struct Mol Biol. 2012 Feb 5;19(3):268-75. doi: 10.1038/nsmb.2237.
8. Chilcote TJ, etal., J Cell Biol. 1995 Apr;129(1):219-31.
9. Chin LS, etal., J Biol Chem 2000 Jan 14;275(2):1191-200.
10. Choi UB, etal., Nat Struct Mol Biol. 2010 Mar;17(3):318-24. doi: 10.1038/nsmb.1763. Epub 2010 Feb 21.
11. Chung I, etal., Neuroscience 2003;116(2):349-57.
12. Coppola T, etal., J Biol Chem 2001 Aug 31;276(35):32756-62.
13. Darios F and Davletov B, Nature. 2006 Apr 6;440(7085):813-7.
14. Darios F, etal., EMBO Rep. 2010 Jul;11(7):528-33. doi: 10.1038/embor.2010.66. Epub 2010 May 21.
15. 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.
16. Deak F, etal., EMBO J. 2006 Jun 21;25(12):2856-66. Epub 2006 Jun 8.
17. Duan P, etal., PLoS One. 2014 May 19;9(5):e97684. doi: 10.1371/journal.pone.0097684. eCollection 2014.
18. Ernst JA and Brunger AT, J Biol Chem. 2003 Mar 7;278(10):8630-6. Epub 2002 Dec 20.
19. Fasshauer D, etal., Biochemistry. 1998 Jul 21;37(29):10354-62.
20. Garcia EP, etal., J Cell Biol 1995 Apr;129(1):105-20.
21. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
22. Gonelle-Gispert C, etal., Biochem J 2002 Nov 15;368(Pt 1):223-32.
23. Graham ME, etal., Ann N Y Acad Sci 2002 Oct;971:210-21.
24. Greber-Platzer S, etal., Neurosci Lett. 2003 Jan 16;336(2):77-80.
25. Hanley JG, etal., Neuron 2002 Mar 28;34(1):53-67.
26. He Y, etal., Biochem J. 2006 Jun 1;396(2):363-9.
27. Hou QL, etal., Biochem Biophys Res Commun. 2006 Sep 8;347(4):955-62. Epub 2006 Jul 25.
28. 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.
29. Ito H, etal., J Neurochem. 2009 Feb;108(4):867-80. doi: 10.1111/j.1471-4159.2008.05849.x.
30. Ji J, etal., J Biol Chem 2002 Jun 7;277(23):20195-204. Epub 2002 Mar 29.
31. Kataoka M, etal., J Neurochem. 2000 May;74(5):2058-66.
32. Koroll M, etal., J Biol Chem 2001 Apr 6;276(14):10646-54.
33. Kwong J, etal., J Cell Sci 2000 Jun;113 ( Pt 12):2273-84.
34. Lang T, etal., EMBO J 2001 May 1;20(9):2202-13.
35. Lang T, etal., J Cell Biol 2002 Aug 19;158(4):751-60.
36. Lee HK, etal., J Neurochem 2002 Jun;81(6):1338-47.
37. Lemonidis K, etal., J Biol Chem. 2015 Sep 4;290(36):21939-50. doi: 10.1074/jbc.M115.657668. Epub 2015 Jul 21.
38. MacDonald PE and Wheeler MB, Diabetologia. 2003 Aug;46(8):1046-62. Epub 2003 Jun 27.
39. Maienschein V, etal., Glia. 1999 May;26(3):233-44.
40. Margittai M, etal., Biochemistry. 2003 Apr 15;42(14):4009-14.
41. Marshall C, etal., Mol Endocrinol. 2005 Jan;19(1):213-24. Epub 2004 Oct 7.
42. Matsuno A, etal., Microsc Res Tech. 2003 Oct 15;62(3):232-9.
43. McMahon HT, etal., Cell 1995 Oct 6;83(1):111-9.
44. MGD data from the GO Consortium
45. NCBI rat LocusLink and RefSeq merged data July 26, 2002
46. Okamoto M, etal., J Biol Chem 1999 Jun 25;274(26):18446-54.
47. Park Y, etal., Nat Struct Mol Biol. 2015 Oct;22(10):815-23. doi: 10.1038/nsmb.3097. Epub 2015 Sep 21.
48. Pellet JB, etal., Eur J Neurosci. 2000 Feb;12(2):621-32.
49. Pobbati AV, etal., J Biol Chem. 2004 Nov 5;279(45):47192-200. Epub 2004 Aug 16.
50. Puffer EB, etal., Biochemistry 2001 Aug 7;40(31):9374-8.
51. Quintanar JL, etal., Endocr Regul. 2004 Mar;38(1):1-6.
52. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
53. RGD automated import pipeline for gene-chemical interactions
54. Ryu JK, etal., Science. 2015 Mar 27;347(6229):1485-9. doi: 10.1126/science.aaa5267.
55. Sakurai T, etal., Bioelectromagnetics. 2004 Apr;25(3):160-6.
56. Salaun C, etal., J Biol Chem. 2005 May 20;280(20):19449-53. Epub 2005 Mar 15.
57. Shin OH, etal., Neuron. 2003 Jan 9;37(1):99-108.
58. Sidor-Kaczmarek J, etal., Folia Morphol (Warsz). 2004 Aug;63(3):285-8.
59. Stein A, etal., Nature. 2009 Jul 23;460(7254):525-8. doi: 10.1038/nature08156. Epub 2009 Jul 1.
60. Steiner P, etal., J Cell Biol. 2002 Jun 24;157(7):1197-209. Epub 2002 Jun 17.
61. Sutton RB, etal., Nature. 1998 Sep 24;395(6700):347-53.
62. Tokumaru H, etal., Brain Cell Biol. 2008 Dec;36(5-6):173-89. doi: 10.1007/s11068-008-9032-9. Epub 2009 Jan 9.
63. Tsuboi T and Fukuda M, J Biol Chem. 2005 Nov 25;280(47):39253-9. Epub 2005 Oct 3.
64. 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.
65. Verderio C, etal., Neuron. 2004 Feb 19;41(4):599-610.
66. 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.
67. Watanabe M, etal., Mol Biol Cell. 2005 Oct;16(10):4519-30. Epub 2005 Jul 19.
68. Weninger K, etal., Structure. 2008 Feb;16(2):308-20. doi: 10.1016/j.str.2007.12.010.
69. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
70. Wu CS, etal., Mol Cell Biol. 2011 Dec;31(24):4874-86. doi: 10.1128/MCB.05593-11. Epub 2011 Oct 10.
71. Yao H, etal., J Neurochem. 2009 Feb;108(4):909-19. doi: 10.1111/j.1471-4159.2008.05834.x. Epub 2008 Dec 10.
72. Yun HJ, etal., Exp Mol Med. 2013 Aug 16;45:e36. doi: 10.1038/emm.2013.68.
73. Zhang L, etal., J Neurocytol. 2000 Jan;29(1):19-30.
74. Zhao M, etal., Nature. 2015 Feb 5;518(7537):61-7. doi: 10.1038/nature14148. Epub 2015 Jan 12.
Additional References at PubMed
PMID:1281490   PMID:7768895   PMID:7961655   PMID:8738135   PMID:9039916   PMID:9168999   PMID:9395480   PMID:10037470   PMID:10336434   PMID:10510169   PMID:11524423   PMID:11533035  
PMID:11753414   PMID:11883949   PMID:12130530   PMID:12145198   PMID:12145319   PMID:12165670   PMID:12398231   PMID:12459461   PMID:12477932   PMID:12730201   PMID:14622145   PMID:14709554  
PMID:15277518   PMID:15355326   PMID:15459722   PMID:15470145   PMID:15489334   PMID:15528447   PMID:15542596   PMID:15647897   PMID:15752769   PMID:15975093   PMID:16385482   PMID:16539689  
PMID:16720719   PMID:16861228   PMID:16888141   PMID:16978778   PMID:17002520   PMID:17293448   PMID:17634366   PMID:17728451   PMID:17886343   PMID:17909947   PMID:18077557   PMID:18381601  
PMID:18385322   PMID:18503508   PMID:18703708   PMID:18721885   PMID:18827011   PMID:18986604   PMID:19482079   PMID:19509185   PMID:19546860   PMID:19661770   PMID:19679075   PMID:19735702  
PMID:19843696   PMID:20002519   PMID:20142423   PMID:20186959   PMID:20519516   PMID:20522554   PMID:20945070   PMID:21040848   PMID:21076040   PMID:21266332   PMID:21401123   PMID:21429935  
PMID:21526988   PMID:21543213   PMID:21558797   PMID:21576241   PMID:21633701   PMID:21646859   PMID:21730064   PMID:21850520   PMID:21926557   PMID:22094010   PMID:22311984   PMID:22411134  
PMID:22871113   PMID:23064108   PMID:23135794   PMID:23395379   PMID:23403573   PMID:23643538   PMID:23699527   PMID:23732542   PMID:23821748   PMID:24327345   PMID:24519330   PMID:24534378  
PMID:24680688   PMID:26888187   PMID:26923581   PMID:26971072   PMID:27693314   PMID:27791016   PMID:28240595   PMID:28412278   PMID:28483813   PMID:28515322   PMID:28634303   PMID:28884870  
PMID:28954226   PMID:29476059   PMID:30377802   PMID:30607888   PMID:31705888   PMID:31705923   PMID:32317281  


Genomics

Comparative Map Data
Snap25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03129,697,408 - 129,788,417 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3129,599,353 - 129,788,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03136,182,051 - 136,269,422 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43124,806,637 - 124,894,653 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13124,712,177 - 124,800,221 (+)NCBI
Celera3122,761,455 - 122,842,679 (+)NCBICelera
Cytogenetic Map3q36NCBI
SNAP25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2010,218,830 - 10,307,418 (+)EnsemblGRCh38hg38GRCh38
GRCh382010,218,830 - 10,307,420 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372010,199,477 - 10,288,068 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362010,147,477 - 10,236,065 (+)NCBINCBI36hg18NCBI36
Build 342010,147,476 - 10,236,065NCBI
Celera2010,269,471 - 10,358,052 (+)NCBI
Cytogenetic Map20p12.2NCBI
HuRef2010,151,237 - 10,239,826 (+)NCBIHuRef
CHM1_12010,200,131 - 10,288,709 (+)NCBICHM1_1
Snap25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392136,555,359 - 136,624,348 (+)NCBIGRCm39mm39
GRCm382136,713,439 - 136,782,428 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2136,713,453 - 136,782,428 (+)EnsemblGRCm38mm10GRCm38
MGSCv372136,539,186 - 136,608,164 (+)NCBIGRCm37mm9NCBIm37
MGSCv362136,404,944 - 136,473,857 (+)NCBImm8
Celera2137,909,643 - 137,978,489 (+)NCBICelera
Cytogenetic Map2F3NCBI
cM Map267.56NCBI
Snap25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541520,133,201 - 20,219,023 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541520,133,361 - 20,218,840 (+)NCBIChiLan1.0ChiLan1.0
SNAP25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12010,164,346 - 10,252,843 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2010,218,358 - 10,252,841 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02010,164,236 - 10,252,856 (+)NCBIMhudiblu_PPA_v0panPan3
SNAP25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2412,004,117 - 12,081,329 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12412,003,005 - 12,081,385 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Snap25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364859,198,744 - 9,279,854 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNAP25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1719,096,140 - 19,227,576 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11719,096,115 - 19,227,580 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21721,669,084 - 21,703,714 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNAP25
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,857,093 - 27,944,487 (-)NCBI
ChlSab1.1 Ensembl227,858,319 - 27,944,496 (-)Ensembl
Snap25
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474111,218,259 - 11,303,406 (+)NCBI

Position Markers
D3M2Mit28  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,787,206 - 129,787,325NCBIRnor6.0
Rnor_5.03136,268,211 - 136,268,330UniSTSRnor5.0
RGSC_v3.43124,893,442 - 124,893,561UniSTSRGSC3.4
Celera3122,841,468 - 122,841,587UniSTS
Cytogenetic Map3q36UniSTS
D3M2Nds33   No map positions available.
D3Wox20  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,787,213 - 129,787,324NCBIRnor6.0
Rnor_5.03136,268,218 - 136,268,329UniSTSRnor5.0
RGSC_v3.43124,893,448 - 124,893,561RGDRGSC3.4
RGSC_v3.43124,893,449 - 124,893,560UniSTSRGSC3.4
RGSC_v3.13124,799,021 - 124,799,134RGD
Celera3122,841,475 - 122,841,586UniSTS
Cytogenetic Map3q36UniSTS
RH 3.4 Map31087.1RGD
RH 3.4 Map31087.1UniSTS
RH 2.0 Map3727.2RGD
D3Kyo3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,787,213 - 129,787,324NCBIRnor6.0
Rnor_5.03136,268,218 - 136,268,329UniSTSRnor5.0
RGSC_v3.43124,893,448 - 124,893,561RGDRGSC3.4
RGSC_v3.43124,893,449 - 124,893,560UniSTSRGSC3.4
RGSC_v3.13124,799,021 - 124,799,134RGD
Celera3122,841,475 - 122,841,586UniSTS
Cytogenetic Map3q36UniSTS
D2Mit28.3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,787,329 - 129,787,585NCBIRnor6.0
Rnor_5.03136,268,334 - 136,268,590UniSTSRnor5.0
RGSC_v3.43124,893,565 - 124,893,821UniSTSRGSC3.4
Celera3122,841,591 - 122,841,847UniSTS
Cytogenetic Map3q36UniSTS
BE107867  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,698,384 - 129,698,556NCBIRnor6.0
Rnor_5.03136,183,027 - 136,183,199UniSTSRnor5.0
RGSC_v3.43124,807,568 - 124,807,740UniSTSRGSC3.4
Celera3122,762,431 - 122,762,603UniSTS
Cytogenetic Map3q36UniSTS
RH 3.4 Map31084.9UniSTS
MARC_11717-11718:1029180244:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03129,787,559 - 129,787,895NCBIRnor6.0
Rnor_5.03136,268,564 - 136,268,900UniSTSRnor5.0
RGSC_v3.43124,893,795 - 124,894,131UniSTSRGSC3.4
Celera3122,841,821 - 122,842,157UniSTS
Cytogenetic Map3q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3117303473141971336Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3120917788141971336Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3120917788141971336Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir128-1rno-miR-128-3pMirtarbaseexternal_infoImmunocytochemistry//Luciferase reporter assay//MiFunctional MTI18381601
Mir146arno-miR-146a-5pMirtarbaseexternal_infoWestern blotNon-Functional MTI18381601

Predicted Target Of
Summary Value
Count of predictions:402
Count of miRNA genes:116
Interacting mature miRNAs:155
Transcripts:ENSRNOT00000007998, ENSRNOT00000008734
Prediction methods:Miranda, 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 13
Medium 1 55 1
Low 3 14 23 8 16 8 8 9 6 12 35 9 8
Below cutoff 22 14 14 2 14 8 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270576 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_030991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07053831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07053837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01025274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF245227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ255912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY315301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM033263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U56261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U56262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000007998   ⟹   ENSRNOP00000007998
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3129,753,742 - 129,787,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000008734   ⟹   ENSRNOP00000008734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3129,599,353 - 129,788,400 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080581   ⟹   ENSRNOP00000072612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3129,753,742 - 129,787,143 (+)Ensembl
RefSeq Acc Id: NM_001270575   ⟹   NP_001257504
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03129,697,408 - 129,788,417 (+)NCBI
Rnor_5.03136,182,051 - 136,269,422 (+)NCBI
Celera3122,761,455 - 122,842,679 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270576   ⟹   NP_001257505
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03129,697,679 - 129,788,417 (+)NCBI
Rnor_5.03136,182,051 - 136,269,422 (+)NCBI
Celera3122,761,726 - 122,842,679 (+)NCBI
Sequence:
RefSeq Acc Id: NM_030991   ⟹   NP_112253
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03129,697,408 - 129,788,417 (+)NCBI
Rnor_5.03136,182,051 - 136,269,422 (+)NCBI
RGSC_v3.43124,806,637 - 124,894,653 (+)RGD
Celera3122,761,455 - 122,842,679 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112253   ⟸   NM_030991
- Peptide Label: isoform b
- UniProtKB: P60881 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257504   ⟸   NM_001270575
- Peptide Label: isoform a
- UniProtKB: P60881 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257505   ⟸   NM_001270576
- Peptide Label: isoform a
- UniProtKB: P60881 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008734   ⟸   ENSRNOT00000008734
RefSeq Acc Id: ENSRNOP00000072612   ⟸   ENSRNOT00000080581
RefSeq Acc Id: ENSRNOP00000007998   ⟸   ENSRNOT00000007998
Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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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
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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
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/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
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 (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
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
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
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
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
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 (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
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)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
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)
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/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 (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 (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 (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:3728 AgrOrtholog
BIND 130538
  130539
  134142
  134143
  134144
  134145
  134455
  134458
  134467
  134468
  134472
Ensembl Genes ENSRNOG00000006037 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007998 UniProtKB/TrEMBL
  ENSRNOP00000008734 UniProtKB/TrEMBL
  ENSRNOP00000072612 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007998 UniProtKB/TrEMBL
  ENSRNOT00000008734 UniProtKB/TrEMBL
  ENSRNOT00000080581 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7314318 IMAGE-MGC_LOAD
InterPro SNAP-25 UniProtKB/Swiss-Prot
  SNAP-25 UniProtKB/TrEMBL
  SNAP-25_dom UniProtKB/TrEMBL
  SNAP25 UniProtKB/Swiss-Prot
  T_SNARE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25012 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105414 IMAGE-MGC_LOAD
NCBI Gene 25012 ENTREZGENE
PANTHER PTHR19305:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNAP-25 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Snap25 PhenoGen
PROSITE T_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART t_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.107689 ENTREZGENE
UniProt A0A0G2K3F2_RAT UniProtKB/TrEMBL
  D4A5W9_RAT UniProtKB/TrEMBL
  F8WG75_RAT UniProtKB/TrEMBL
  P60881 ENTREZGENE
  Q2XTA5_RAT UniProtKB/TrEMBL
  SNP25_RAT UniProtKB/Swiss-Prot
UniProt Secondary P13795 UniProtKB/Swiss-Prot
  P36974 UniProtKB/Swiss-Prot
  P70557 UniProtKB/Swiss-Prot
  P70558 UniProtKB/Swiss-Prot
  Q8IXK3 UniProtKB/Swiss-Prot
  Q96FM2 UniProtKB/Swiss-Prot
  Q9BR45 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Snap25  synaptosome associated protein 25  Snap25  synaptosomal-associated protein 25  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Snap25  synaptosomal-associated protein 25    synaptosomal-associated protein  Name updated 1299863 APPROVED
2002-06-10 Snap25  synaptosomal-associated protein      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function interacts with other proteins including the C2 domain of Rim, participates with sytaxin 1 in locating cholesterol-dependent clusters in the plasmalemma, at which secretory vesicles preferentially dock and fuse 68723
gene_function interacts with other proteins including the C2 domain of Rim, participates with sytaxin 1 in locating cholesterol-dependent clusters in the plasmalemma, at which secretory vesicles preferentially dock and fuse 68912
gene_physical_interaction interacts with K(DR) channel subtype, K(V)1.1 1299041
gene_physical_interaction interacts with C(2) domains of Rab3-interacting molecule (RIM) and this interaction is modulated by calcium 68912
gene_process inhibits delayed rectifier K+ channel K(V)1.1 in insulinoma cells which likely regulates secretion 1299041
gene_process may participate in neurotransmitter release 1299042
gene_process may play a role in apical targeting of secretory vesicles in choroidal epithelium 1299043
gene_product member of the soluble NSF attachment protein (SNAP) receptor (SNARE) superfamily that mediates membrane fusion 730202
gene_protein 25 kDa 68723
gene_protein 25 kDa 68912
gene_transcript isoform SNAP-25b is present only in differentiated cells and isoform SNAP-25a is present in both differentiated and undifferentiated cells 1299042