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: Enables several functions, including calcium-dependent protein binding activity; syntaxin-1 binding activity; and transmembrane transporter binding activity. Involved in several processes, including SNARE complex assembly; long-term memory; and signal release. Located in several cellular components, including axonal growth cone; lamellipodium; and presynaptic active zone membrane. Is anchored component of presynaptic membrane. Part of several cellular components, including synaptobrevin 2-SNAP-25-syntaxin-1a complex; synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex; and synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex. Is active in glutamatergic synapse. 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23124,041,898 - 124,123,761 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3124,041,898 - 124,123,760 (+)Ensembl
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)
aristolochic acid  (ISO)
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)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chlordecone  (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)
deguelin  (ISO)
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)
ivermectin  (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)
nitrofen  (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
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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   PMID:32357304   PMID:32367505   PMID:33468652  


Genomics

Comparative Map Data
Snap25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23124,041,898 - 124,123,761 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3124,041,898 - 124,123,760 (+)Ensembl
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
GRCh372010,199,478 - 10,288,066 (+)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_12010,200,162 - 10,288,707 (+)NCBICHM1_1
Snap25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392136,555,359 - 136,624,348 (+)NCBIGRCm39mm39
GRCm39 Ensembl2136,555,373 - 136,624,348 (+)Ensembl
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
CanFam3.12412,003,005 - 12,081,385 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2412,004,117 - 12,081,329 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2411,821,959 - 11,900,304 (-)NCBI
ROS_Cfam_1.02412,414,152 - 12,492,563 (-)NCBI
UMICH_Zoey_3.12412,021,341 - 12,099,876 (-)NCBI
UNSW_CanFamBas_1.02412,120,883 - 12,199,168 (-)NCBI
UU_Cfam_GSD_1.02412,463,988 - 12,542,509 (-)NCBI
Snap25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640160,767,380 - 160,848,503 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,857,093 - 27,944,487 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl227,858,319 - 27,944,496 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607116,634,204 - 16,722,155 (+)NCBIVero_WHO_p1.0
Snap25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474111,218,259 - 11,303,406 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D3M2Mit28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23124,122,549 - 124,122,669 (+)MAPPERmRatBN7.2
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
mRatBN7.23124,122,556 - 124,122,668 (+)MAPPERmRatBN7.2
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
RH 3.4 Map31087.1UniSTS
RH 3.4 Map31087.1RGD
RH 2.0 Map3727.2RGD
Cytogenetic Map3q36UniSTS
D3Kyo3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23124,122,556 - 124,122,668 (+)MAPPERmRatBN7.2
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
mRatBN7.23124,122,672 - 124,122,929 (+)MAPPERmRatBN7.2
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
mRatBN7.23124,042,873 - 124,043,046 (+)MAPPERmRatBN7.2
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
RH 3.4 Map31084.9UniSTS
Cytogenetic Map3q36UniSTS
MARC_11717-11718:1029180244:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23124,122,902 - 124,123,239 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
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)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
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)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
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)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat

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
  XM_039104314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide 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
  JACYVU010000118 (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
mRatBN7.2 Ensembl3124,041,898 - 124,123,760 (+)Ensembl
Rnor_6.0 Ensembl3129,753,742 - 129,787,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000008734   ⟹   ENSRNOP00000008734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3124,090,016 - 124,123,760 (+)Ensembl
Rnor_6.0 Ensembl3129,599,353 - 129,788,400 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080581   ⟹   ENSRNOP00000072612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3124,041,898 - 124,123,760 (+)Ensembl
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
mRatBN7.23124,041,898 - 124,123,761 (+)NCBI
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
mRatBN7.23124,042,169 - 124,123,761 (+)NCBI
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
mRatBN7.23124,041,898 - 124,123,761 (+)NCBI
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:
RefSeq Acc Id: XM_039104314   ⟹   XP_038960242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23124,042,204 - 124,123,761 (+)NCBI
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
RefSeq Acc Id: XP_038960242   ⟸   XM_039104314
- Peptide Label: isoform X1
Protein Domains
t-SNARE coiled-coil homology

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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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)
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
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