Vamp1 (vesicle-associated membrane protein 1) - Rat Genome Database

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Gene: Vamp1 (vesicle-associated membrane protein 1) Rattus norvegicus
Analyze
Symbol: Vamp1
Name: vesicle-associated membrane protein 1
RGD ID: 3948
Description: Predicted to enable SNAP receptor activity and syntaxin binding activity. Predicted to be involved in SNARE complex assembly; regulation of synaptic vesicle fusion to presynaptic active zone membrane; and synaptic vesicle priming. Located in terminal bouton. Is active in presynapse. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome and spastic ataxia 1. Orthologous to human VAMP1 (vesicle associated membrane protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Syb1; synaptobrevin 1; synaptobrevin-1; VAMP-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84159,698,894 - 159,705,582 (+)NCBIGRCr8
mRatBN7.24158,012,634 - 158,019,350 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,012,663 - 158,019,349 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4164,241,975 - 164,248,577 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,024,891 - 160,031,493 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04158,660,913 - 158,667,515 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04157,726,941 - 157,733,644 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,726,941 - 157,733,643 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,743,851 - 224,750,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,333,661 - 161,340,447 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14161,578,698 - 161,583,642 (+)NCBI
Celera4146,749,782 - 146,756,446 (+)NCBICelera
RH 3.4 Map41003.9RGD
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
1,2-dichloroethane  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
chloroethene  (ISO)
choline  (ISO)
cisplatin  (ISO)
clozapine  (EXP)
copper(II) sulfate  (ISO)
coumarin  (ISO)
Cuprizon  (EXP)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
ethanol  (EXP,ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gamma-tocopherol  (ISO)
gentamycin  (EXP)
haloperidol  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
MeIQx  (ISO)
methimazole  (EXP)
methylisothiazolinone  (ISO)
nickel sulfate  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
tert-butyl hydroperoxide  (ISO)
titanium dioxide  (ISO)
tocopherol  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. The specificity of SNARE pairing in biological membranes is mediated by both proof-reading and spatial segregation. Bethani I, etal., EMBO J. 2007 Sep 5;26(17):3981-92. Epub 2007 Aug 23.
2. Changes in mRNA for VAMPs following facial nerve transection. Che YH, etal., J Chem Neuroanat 2002 Jul;24(2):147-52.
3. Expression of two membrane fusion proteins, synaptosome-associated protein of 25 kDa and vesicle-associated membrane protein, in choroid plexus epithelium. Chung I, etal., Neuroscience 2003;116(2):349-57.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
7. Tissue-specific alternative RNA splicing of rat vesicle-associated membrane protein-1 (VAMP-1). Mandic R, etal., Gene 1997 Oct 15;199(1-2):173-9.
8. Isolation and characterization of a dual prenylated Rab and VAMP2 receptor. Martincic I, etal., J Biol Chem 1997 Oct 24;272(43):26991-8.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
16. VAMP-1: a synaptic vesicle-associated integral membrane protein. Trimble WS, etal., Proc Natl Acad Sci U S A. 1988 Jun;85(12):4538-42.
17. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
Additional References at PubMed
PMID:1299100   PMID:2472388   PMID:8889548   PMID:11391393   PMID:12477932   PMID:16169186   PMID:16539689   PMID:17360966   PMID:17666428   PMID:18655825   PMID:20085749   PMID:20406821  
PMID:20801128   PMID:21330375   PMID:22871113   PMID:23699527   PMID:24534378   PMID:24604356   PMID:25010769   PMID:26888187   PMID:27791016   PMID:28314111   PMID:28477408   PMID:29476059  
PMID:31962145  


Genomics

Comparative Map Data
Vamp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84159,698,894 - 159,705,582 (+)NCBIGRCr8
mRatBN7.24158,012,634 - 158,019,350 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4158,012,663 - 158,019,349 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4164,241,975 - 164,248,577 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04160,024,891 - 160,031,493 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04158,660,913 - 158,667,515 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04157,726,941 - 157,733,644 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,726,941 - 157,733,643 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,743,851 - 224,750,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,333,661 - 161,340,447 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14161,578,698 - 161,583,642 (+)NCBI
Celera4146,749,782 - 146,756,446 (+)NCBICelera
RH 3.4 Map41003.9RGD
Cytogenetic Map4q42NCBI
VAMP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38126,462,237 - 6,470,677 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl126,462,237 - 6,470,677 (-)EnsemblGRCh38hg38GRCh38
GRCh37126,571,403 - 6,579,843 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,441,664 - 6,450,104 (-)NCBINCBI36Build 36hg18NCBI36
Build 34126,441,666 - 6,450,104NCBI
Celera128,188,292 - 8,196,732 (-)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef126,425,592 - 6,434,004 (-)NCBIHuRef
CHM1_1126,570,277 - 6,578,717 (-)NCBICHM1_1
T2T-CHM13v2.0126,472,621 - 6,481,015 (-)NCBIT2T-CHM13v2.0
Vamp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396125,192,544 - 125,199,269 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6125,192,514 - 125,222,927 (+)EnsemblGRCm39 Ensembl
GRCm386125,215,581 - 125,222,306 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6125,215,551 - 125,245,964 (+)EnsemblGRCm38mm10GRCm38
MGSCv376125,165,599 - 125,172,324 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366125,181,200 - 125,187,922 (+)NCBIMGSCv36mm8
Celera6126,885,383 - 126,892,110 (+)NCBICelera
Cytogenetic Map6F3NCBI
cM Map659.32NCBI
Vamp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,117,367 - 4,124,149 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,117,367 - 4,124,149 (-)NCBIChiLan1.0ChiLan1.0
VAMP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21012,023,662 - 12,032,366 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,020,416 - 12,029,162 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0126,592,688 - 6,601,317 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1126,486,475 - 6,518,459 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl126,509,762 - 6,518,459 (-)Ensemblpanpan1.1panPan2
VAMP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12738,518,978 - 38,526,361 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2738,518,974 - 38,559,455 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha278,090,305 - 8,097,691 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02738,872,706 - 38,880,082 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2738,872,951 - 38,880,078 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12738,745,477 - 38,752,859 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02738,786,894 - 38,794,280 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0277,569,199 - 7,576,586 (-)NCBIUU_Cfam_GSD_1.0
Vamp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945102,630,494 - 102,637,244 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367091,297,743 - 1,304,899 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367091,297,820 - 1,304,793 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VAMP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1564,181,496 - 64,188,275 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2566,643,057 - 66,649,800 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VAMP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1116,510,717 - 6,520,429 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660631,711,975 - 1,721,326 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vamp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248603,213,474 - 3,219,359 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248603,212,549 - 3,219,354 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vamp1
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:312
Count of miRNA genes:187
Interacting mature miRNAs:241
Transcripts:ENSRNOT00000025081, ENSRNOT00000026012
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)426775591168368347Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4157680158158841762Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat

Markers in Region
BE292615  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,019,003 - 158,019,116 (+)MAPPERmRatBN7.2
Rnor_6.04157,733,298 - 157,733,410NCBIRnor6.0
Rnor_5.04224,750,094 - 224,750,206UniSTSRnor5.0
RGSC_v3.44161,340,101 - 161,340,213UniSTSRGSC3.4
Celera4146,756,100 - 146,756,212UniSTS
Cytogenetic Map4q42UniSTS
Vamp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,019,065 - 158,019,291 (+)MAPPERmRatBN7.2
Rnor_6.04157,733,360 - 157,733,585NCBIRnor6.0
Rnor_5.04224,750,156 - 224,750,381UniSTSRnor5.0
RGSC_v3.44161,340,163 - 161,340,388UniSTSRGSC3.4
Celera4146,756,162 - 146,756,387UniSTS
Cytogenetic Map4q42UniSTS
RH94634  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24158,017,434 - 158,017,594 (+)MAPPERmRatBN7.2
Rnor_6.04157,731,723 - 157,731,882NCBIRnor6.0
Rnor_5.04224,748,519 - 224,748,678UniSTSRnor5.0
RGSC_v3.44161,338,526 - 161,338,685UniSTSRGSC3.4
Celera4146,754,525 - 146,754,684UniSTS
RH 3.4 Map41003.9UniSTS
Cytogenetic Map4q42UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000025081   ⟹   ENSRNOP00000025081
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,012,663 - 158,019,349 (+)Ensembl
Rnor_6.0 Ensembl4157,726,941 - 157,733,643 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096098   ⟹   ENSRNOP00000076937
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,012,738 - 158,019,321 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000097145   ⟹   ENSRNOP00000080681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4158,015,629 - 158,017,615 (+)Ensembl
RefSeq Acc Id: NM_013090   ⟹   NP_037222
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84159,698,894 - 159,705,582 (+)NCBI
mRatBN7.24158,012,663 - 158,019,350 (+)NCBI
Rnor_6.04157,726,941 - 157,733,644 (+)NCBI
Rnor_5.04224,743,851 - 224,750,440 (+)NCBI
RGSC_v3.44161,333,661 - 161,340,447 (+)RGD
Celera4146,749,782 - 146,756,446 (+)RGD
Sequence:
RefSeq Acc Id: NP_037222   ⟸   NM_013090
- UniProtKB: Q56A22 (UniProtKB/Swiss-Prot),   O09025 (UniProtKB/Swiss-Prot),   A6YSN3 (UniProtKB/Swiss-Prot),   Q8CH14 (UniProtKB/Swiss-Prot),   Q63666 (UniProtKB/Swiss-Prot),   A6ILT1 (UniProtKB/TrEMBL),   A6ILS9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000025081   ⟸   ENSRNOT00000025081
Ensembl Acc Id: ENSRNOP00000080681   ⟸   ENSRNOT00000097145
Ensembl Acc Id: ENSRNOP00000076937   ⟸   ENSRNOT00000096098
Protein Domains
v-SNARE coiled-coil homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63666-F1-model_v2 AlphaFold Q63666 1-118 view protein structure

Transcriptome

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

Promoters
RGD ID:13693406
Promoter ID:EPDNEW_R3931
Type:single initiation site
Name:Vamp1_1
Description:vesicle-associated membrane protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04157,726,931 - 157,726,991EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3948 AgrOrtholog
BioCyc Gene G2FUF-43004 BioCyc
Ensembl Genes ENSRNOG00000019219 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025081.6 UniProtKB/Swiss-Prot
  ENSRNOT00000096098.1 UniProtKB/Swiss-Prot
  ENSRNOT00000097145.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7313343 IMAGE-MGC_LOAD
InterPro Synaptobrevin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Synaptobrevin/VAMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V_SNARE_CC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25624 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105480 IMAGE-MGC_LOAD
NCBI Gene 25624 ENTREZGENE
PANTHER PTHR45701 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Synaptobrevin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vamp1 PhenoGen
PIRSF Synaptobrevin_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS SYNAPTOBREVN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SYNAPTOBREVIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019219 RatGTEx
Superfamily-SCOP SNARE fusion complex UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204051
UniProt A0A8I5ZR85_RAT UniProtKB/TrEMBL
  A6ILS9 ENTREZGENE, UniProtKB/TrEMBL
  A6ILT1 ENTREZGENE, UniProtKB/TrEMBL
  A6YSN3 ENTREZGENE
  O09025 ENTREZGENE
  Q56A22 ENTREZGENE
  Q63666 ENTREZGENE
  Q8CH14 ENTREZGENE
  VAMP1_RAT UniProtKB/Swiss-Prot
UniProt Secondary A6YSN3 UniProtKB/Swiss-Prot
  O09025 UniProtKB/Swiss-Prot
  Q56A22 UniProtKB/Swiss-Prot
  Q8CH14 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2001-06-22 Vamp1  Vesicle-associated membrane protein 1      Name updated 67952 APPROVED
2001-06-22 Syb1  Synaptobrevin 1      Symbol withdrawn, duplicate of Vamp1 (RGD:3948) 67952 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_expression protein and mRNA are expressed in the choroid plexus, however, alternative splce form Vamp-1b is not detected in this tissue 1299043
gene_transcript Vamp-1b is produced by alternative pre-mRNA splicing 1299100