Advanced Search (OLGA)

Gene: Vamp3 (vesicle-associated membrane protein 3) Rattus norvegicus

Analyze

Symbol:

Vamp3

Name:

vesicle-associated membrane protein 3

RGD ID:

61880

Description:

Enables syntaxin-1 binding activity. Involved in protein-containing complex assembly. Located in apical plasma membrane; clathrin-coated vesicle membrane; and recycling endosome. Part of SNARE complex. Is active in synaptic vesicle membrane. Orthologous to human VAMP3 (vesicle associated membrane protein 3); PARTICIPATES IN autophagy pathway; phagocytosis pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 3H-1,2-dithiole-3-thione; 4,4'-sulfonyldiphenol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

CEB; cellubrevin; MGC108618; synaptobrevin-3; VAMP-3

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	VAMP3 (vesicle associated membrane protein 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Vamp3 (vesicle-associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vamp3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VAMP3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VAMP3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vamp3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VAMP3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VAMP3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vamp3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Vamp3 (vesicle associated membrane protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	VAMP2 (vesicle associated membrane protein 2)	HGNC	OrthoDB
Homo sapiens (human):	VAMP1 (vesicle associated membrane protein 1)	HGNC	OrthoDB
Homo sapiens (human):	KNDC1 (kinase non-catalytic C-lobe domain containing 1)	HGNC	OMA
Alliance orthologs ³
Mus musculus (house mouse):	Vamp3 (vesicle-associated membrane protein 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	VAMP3 (vesicle associated membrane protein 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	vamp3 (vesicle-associated membrane protein 3 (cellubrevin))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snb-1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	snb-1	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	SNC1	Alliance	DIOPT (InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SNC1	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	SNC2	Alliance	DIOPT (InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SNC2	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Syb	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	nSyb	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snb-2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	vamp3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	166,780,927 - 166,791,522 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	5	166,780,929 - 166,791,549 (-)	Ensembl				GRCr8
mRatBN7.2	5	161,498,109 - 161,508,704 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	161,498,109 - 161,508,751 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	5	164,214,807 - 164,225,406 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	166,031,426 - 166,042,030 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	165,993,451 - 166,004,050 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	168,126,157 - 168,136,628 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	168,126,157 - 168,136,666 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	5	171,703,252 - 171,713,723 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	5	168,190,569 - 168,201,165 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	5	159,750,283 - 159,760,878 (-)	NCBI		Celera
RGSC_v3.1	5	168,200,756 - 168,386,085 (-)	NCBI
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trimethylbenzene (EXP)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,6-dimethoxyphenol (ISO)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (EXP,ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (EXP,ISO)

cadmium dichloride (EXP)

caffeine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

coumarin (ISO)

crocidolite asbestos (ISO)

diethylstilbestrol (EXP)

ethanol (EXP)

formaldehyde (ISO)

furfural (ISO)

gentamycin (EXP)

ivermectin (ISO)

methylseleninic acid (ISO)

paracetamol (ISO)

pirinixic acid (ISO)

resveratrol (ISO)

sarin (ISO)

sodium arsenite (ISO)

sodium chloride (ISO)

temozolomide (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

valproic acid (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

calcium-ion regulated exocytosis (ISO)

cellular response to type II interferon (ISO)

Golgi to plasma membrane protein transport (ISO)

mucus secretion (ISO)

negative regulation of secretion by cell (IEA,ISO)

positive regulation of immunoglobulin production (ISO)

positive regulation of receptor recycling (ISO,ISS)

protein transport (IEA)

protein-containing complex assembly (IDA)

regulation of histamine secretion by mast cell (ISO)

retrograde transport, endosome to Golgi (IEA,ISO,ISS)

SNARE complex assembly (IBA,ISO)

substrate adhesion-dependent cell spreading (ISO,ISS)

vesicle fusion (IBA)

vesicle-mediated transport (IEA,ISO,ISS)

Cellular Component

apical plasma membrane (IDA)

cell surface (ISO)

clathrin-coated vesicle (IEA,ISO)

clathrin-coated vesicle membrane (IDA)

cytoplasmic vesicle (ISO)

cytosol (IEA,ISO)

early endosome (ISO)

early endosome membrane (IEA)

endomembrane system (IEA)

intracellular vesicle (IDA)

membrane (IEA)

neuron projection (IEA)

perinuclear region of cytoplasm (ISO)

phagocytic vesicle (ISO)

plasma membrane (IBA,ISO,ISS)

recycling endosome (IDA,IEA,ISO)

recycling endosome membrane (IEA)

secretory granule (ISO)

SNARE complex (IBA,IDA,IEA,ISO)

synapse (IEA)

synaptic vesicle membrane (EXP,IDA,IEP)

Molecular Function

protein binding (IPI,ISO)

SNAP receptor activity (IBA)

SNARE binding (IPI)

syntaxin-1 binding (IBA,IPI)

Molecular Pathway Annotations Click to see Annotation Detail View

autophagy pathway (ISO)

phagocytosis pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Export of cellubrevin from the endoplasmic reticulum is controlled by BAP31.	Annaert WG, etal., J Cell Biol. 1997 Dec 15;139(6):1397-410.
2.	Changes in mRNA for VAMPs following facial nerve transection.	Che YH, etal., J Chem Neuroanat 2002 Jul;24(2):147-52.
3.	Cellubrevin and synaptobrevins: similar subcellular localization and biochemical properties in PC12 cells.	Chilcote TJ, etal., J Cell Biol. 1995 Apr;129(1):219-31.
4.	Water channel-carrying vesicles in the rat IMCD contain cellubrevin.	Franki N, etal., Am J Physiol. 1995 Sep;269(3 Pt 1):C797-801.
5.	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.
6.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
7.	Identification of a novel Bves function: regulation of vesicular transport.	Hager HA, etal., EMBO J. 2010 Feb 3;29(3):532-45. doi: 10.1038/emboj.2009.379. Epub 2010 Jan 7.
8.	Syntaxin 2 and endobrevin are required for the terminal step of cytokinesis in mammalian cells.	Low SH, etal., Dev Cell 2003 May;4(5):753-9.
9.	A plethora of presynaptic proteins associated with ATP-storing organelles in cultured astrocytes.	Maienschein V, etal., Glia. 1999 May;26(3):233-44.
10.	Cellubrevin is a ubiquitous tetanus-toxin substrate homologous to a putative synaptic vesicle fusion protein.	McMahon HT, etal., Nature 1993 Jul 22;364(6435):346-9.
11.	Overview of macroautophagy regulation in mammalian cells.	Mehrpour M, etal., Cell Res. 2010 Jul;20(7):748-62. Epub 2010 Jun 15.
12.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
13.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
14.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
15.	GOA pipeline	RGD automated data pipeline
16.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
17.	SNAP-23 participates in SNARE complex assembly in rat adipose cells.	St-Denis JF, etal., Biochem J 1999 Mar 15;338 ( Pt 3):709-15.
18.	Molecular anatomy of a trafficking organelle.	Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
19.	A tubular endosomal fraction from rat liver: biochemical evidence of receptor sorting by default.	Verges M, etal., Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10146-51.

Additional References at PubMed

PMID:12130530	PMID:12477932	PMID:15489334	PMID:15920476	PMID:18195106	PMID:18253931	PMID:18321981	PMID:18505797	PMID:19061864	PMID:19144319	PMID:19478182	PMID:20582536
PMID:20847273	PMID:21151919	PMID:22144578	PMID:22589474	PMID:22871113	PMID:24055037	PMID:25008321	PMID:26629404	PMID:27551042	PMID:29476059

Genomics

Comparative Map Data

Vamp3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	166,780,927 - 166,791,522 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	5	166,780,929 - 166,791,549 (-)	Ensembl				GRCr8
mRatBN7.2	5	161,498,109 - 161,508,704 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	161,498,109 - 161,508,751 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	5	164,214,807 - 164,225,406 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	166,031,426 - 166,042,030 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	165,993,451 - 166,004,050 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	168,126,157 - 168,136,628 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	168,126,157 - 168,136,666 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	5	171,703,252 - 171,713,723 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	5	168,190,569 - 168,201,165 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	5	159,750,283 - 159,760,878 (-)	NCBI		Celera
RGSC_v3.1	5	168,200,756 - 168,386,085 (-)	NCBI
Cytogenetic Map	5	q36	NCBI

VAMP3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	7,771,296 - 7,781,432 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	7,771,296 - 7,781,432 (+)	Ensembl			hg38	GRCh38
GRCh37	1	7,831,356 - 7,841,492 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	7,753,916 - 7,764,079 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	7,765,594 - 7,775,757	NCBI
Celera	1	6,939,057 - 6,949,218 (+)	NCBI		Celera
Cytogenetic Map	1	p36.23	NCBI
HuRef	1	6,979,774 - 6,989,939 (+)	NCBI		HuRef
CHM1_1	1	7,819,031 - 7,829,192 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	7,302,342 - 7,312,478 (+)	NCBI		T2T-CHM13v2.0

Vamp3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	151,131,762 - 151,142,410 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	151,131,757 - 151,142,420 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	4	151,047,305 - 151,057,953 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	151,047,300 - 151,057,963 (-)	Ensembl			mm10	GRCm38
MGSCv37	4	150,421,414 - 150,432,062 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	4	149,891,105 - 149,901,753 (-)	NCBI		MGSCv36	mm8
Celera	4	153,323,081 - 153,333,830 (-)	NCBI		Celera
Cytogenetic Map	4	E2	NCBI
cM Map	4	81.53	NCBI

Vamp3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955486	5,103,106 - 5,112,176 (-)	Ensembl
ChiLan1.0	NW_004955486	5,103,228 - 5,112,157 (-)	NCBI	ChiLan1.0	ChiLan1.0

VAMP3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	220,444,847 - 220,455,016 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	219,085,975 - 219,096,144 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	6,534,115 - 6,544,275 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	7,782,810 - 7,792,958 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

VAMP3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	61,430,711 - 61,440,626 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	61,430,740 - 61,439,063 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	61,439,454 - 61,449,379 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	61,647,556 - 61,657,492 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	5	61,647,531 - 61,657,492 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	5	61,646,808 - 61,656,746 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	61,511,261 - 61,521,200 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	61,914,945 - 61,924,879 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Vamp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	31,793,913 - 31,802,660 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936623	2,280,534 - 2,287,898 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VAMP3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	6	68,473,921 - 68,482,438 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

VAMP3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	123,973,672 - 123,984,230 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	123,971,992 - 123,984,187 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666054	28,008,620 - 28,019,197 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vamp3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624818	4,009,991 - 4,019,728 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624818	4,010,130 - 4,019,695 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Vamp3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	1	9,714,347 - 9,725,436 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Vamp3
41 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	524
Count of miRNA genes:	258
Interacting mature miRNAs:	310
Transcripts:	ENSRNOT00000051554
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	55124766	172190305	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	130249266	172190305	Rat
631272	Lanf1	Left ventricular atrial natriuretic factor QTL 1	12		heart left ventricle natriuretic peptide A amount (VT:0010596)	heart left ventricle natriuretic peptide A level (CMO:0002165)	5	156396728	167181764	Rat
1354583	Despr3	Despair related QTL3	4.98	0.0002	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	5	132930505	172190305	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	141212838	172190305	Rat
1300119	Bp180	Blood pressure QTL 180	3.82		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	149642129	171146538	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	131708216	172190305	Rat
1549904	Neuinf1	Neuroinflammation QTL 1	3	0	nervous system integrity trait (VT:0010566)	blood T lymphocyte count (CMO:0000110)	5	160111176	171146538	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	99905133	172190305	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	133789363	172190305	Rat
1331803	Rf32	Renal function QTL 32	2.798		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	134369199	172190305	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	136631198	172190305	Rat
1354631	Swd2	Spike wave discharge measurement QTL 2	3.64	0.0002	brain electrophysiology trait (VT:0010557)	brain total spike-and-wave discharge duration (CMO:0001740)	5	156396728	172190305	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	133081618	172190305	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	138002522	170842766	Rat
1581505	Rf54	Renal function QTL 54			kidney physiology trait (VT:0002136)	kidney 20-HETE level (CMO:0001854)	5	133270647	172190305	Rat
1298090	Bp155	Blood pressure QTL 155	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	156289283	171137955	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	160071170	172129029	Rat
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	141764300	172190305	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	133081618	172190305	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	133789363	172190305	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	148093485	172129029	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	125969677	172190305	Rat

Markers in Region

RH128595

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	161,498,200 - 161,498,392 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	168,126,249 - 168,126,440	NCBI	Rnor6.0
Rnor_5.0	5	171,703,344 - 171,703,535	UniSTS	Rnor5.0
RGSC_v3.4	5	168,190,661 - 168,190,852	UniSTS	RGSC3.4
Celera	5	159,750,375 - 159,750,566	UniSTS
RH 3.4 Map	5	1131.9	UniSTS
Cytogenetic Map	5	q36	UniSTS

RH133944

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	106,511,071 - 106,511,278 (+)	MAPPER	mRatBN7.2
mRatBN7.2	5	161,498,883 - 161,499,097 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	168,126,932 - 168,127,145	NCBI	Rnor6.0
Rnor_6.0	10	110,437,315 - 110,437,521	NCBI	Rnor6.0
Rnor_5.0	10	110,023,973 - 110,024,179	UniSTS	Rnor5.0
Rnor_5.0	5	171,704,027 - 171,704,240	UniSTS	Rnor5.0
RGSC_v3.4	5	168,191,344 - 168,191,557	UniSTS	RGSC3.4
RGSC_v3.4	10	110,467,748 - 110,467,954	UniSTS	RGSC3.4
Celera	10	105,049,293 - 105,049,499	UniSTS
Celera	5	159,751,058 - 159,751,271	UniSTS
RH 3.4 Map	5	1130.2	UniSTS
Cytogenetic Map	5	q36	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

RH143401

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	161,508,030 - 161,508,179 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	168,135,955 - 168,136,103	NCBI	Rnor6.0
Rnor_5.0	5	171,713,050 - 171,713,198	UniSTS	Rnor5.0
RGSC_v3.4	5	168,200,491 - 168,200,639	UniSTS	RGSC3.4
Celera	5	159,760,205 - 159,760,353	UniSTS
RH 3.4 Map	5	1129.6	UniSTS
Cytogenetic Map	5	q36	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_057097	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC088119	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ217862	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	S63830	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000051554 ⟹ ENSRNOP00000048364

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	5	166,780,929 - 166,789,512 (-)	Ensembl
mRatBN7.2 Ensembl	5	161,498,177 - 161,508,751 (-)	Ensembl
Rnor_6.0 Ensembl	5	168,126,157 - 168,136,666 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000108568 ⟹ ENSRNOP00000082314

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	161,498,109 - 161,506,856 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000110400 ⟹ ENSRNOP00000083016

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	5	166,782,355 - 166,789,417 (-)	Ensembl
mRatBN7.2 Ensembl	5	161,500,075 - 161,506,599 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000146635 ⟹ ENSRNOP00000103069

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	5	166,782,355 - 166,791,549 (-)	Ensembl

RefSeq Acc Id:

NM_057097 ⟹ NP_476438

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	166,780,927 - 166,791,522 (-)	NCBI
mRatBN7.2	5	161,498,109 - 161,508,704 (-)	NCBI
Rnor_6.0	5	168,126,157 - 168,136,628 (-)	NCBI
Rnor_5.0	5	171,703,252 - 171,713,723 (-)	NCBI
RGSC_v3.4	5	168,190,569 - 168,201,165 (-)	RGD
Celera	5	159,750,283 - 159,760,878 (-)	RGD

Sequence:

show sequence

CGCAAGTCCACGGACCCTCGGCCATTCGCTGCCGCTGCCGCCGCCGCCAAAATGTCTACAGGGG
TGCCTTCAGGGTCCAGTGCTGCCACTGGCAGTAATCGAAGACTCCAGCAGACACAGAATCAAGT
AGATGAGGTGGTGGACATCATGAGAGTCAATGTGGATAAGGTGTTAGAAAGAGACCAGAAGCTC
TCAGAGCTAGACGACCGCGCAGATGCACTGCAGGCAGGCGCCTCGCAGTTTGAAACAAGTGCTG
CCAAGTTGAAGAGAAAGTATTGGTGGAAGAACTGCAAGATGTGGGCGATAGGGATCAGTGTCCT
GGTGATTATTGTCATTATCATCATTGTGTGGTGTGTCTCTTAATGAAGAACAGAGGAAATGAAG
CCTGACGGCAGGATCTTCTTCGAGACTTTCTACTTAGAACTGCGTGTTGTCGCACTTCCCTGTT
GTTTTTTTTTTTTCCCAAATGATTATTTGTGTTAGTTTACATACAGTTCAGTGCCTAGAAAATG
TGCCTTTGTTTTTCATATACACTCGAGGTGTGACCTGCCCTGCCCACATTTTGCACAGTGCCTT
TACAGATTTATGGACTGGGAAAGAGGACTTGTGTGTTTCAGAGTGCTGAGATCTAGGTGGATGT
TGTCACTGATGGCTTGTGGATTCAAGGAAGAGGATTTTGTTCAAGTCAGCTGTCCCCACACCTA
ACATGGACTTCAAAACCACAGTTTAAACCTTTGGGTAATTAGATTCCCAACTTGGACCTTCCAA
GAAGAACACTACTGCCTAACAAAAATCAGTGACAACAGCAGGGCGTGCCTTATTTTGATAACTA
GGTAACTTTTCATTAAGAGTACTTTTGTAAGCACTACCGACCCCGCTGTATTTAAGATGCTGGT
GAAGAGCTCATGCTCTTATGTTAGATACGGAGATGTTCACTTTCTAGTTCTTGTTGTGTATCAC
TTCTAAAACAGTATTTTAATCAGAAATAACCCTTTAGGAAGTTTTTATAGAACTGTGACCAAAG
TTTCTATTTTGCCAAAAGTTAAATACAAATGAATTGTCCATAAGTTTGTCCCCCAGTAGTAAAT
TCAAATAAGTGCCAAGTGTAACTCAAGGTGCCCTTTAAGAAAAAATGTTAGTACTGTCTGAGCC
CGCAGCATCTTGACAGTCCTTCCTGTGGAATGCTGTAGGTACAGCTTCTCATCCTGATGTGGTT
TCTTTCCTAGAGCGATAGAGGTGACCTCAAATCACACCTGTATGCAAGATAGTAGTTTGCAGAC
TGCACTAGCCTGTGGCCACTAGTGTGATGAGAGCAGCATCTGAAGCCTCACAAAGGCAACAGTC
TGCACAGAGTTCTGGGAGACTGTGGCAGTGCCACCAGGATGTCCTGAAATGTGTGTCTGTGTGC
AAAGCAGCATTAGCCAAAATGTCATAGGATCTGGTTCTAGTTTTTTTTATCTGATCCCCTAACA
TTACTGAAACAAAACAAGTGTTGAAGACATGCCTTGCCACATAGCTAGGGCCTCTGTCCTGGTC
TGACCCCACAACTTTGGTGCTGTCTCCTCGTACTCTGTCCCATGTAAGTCGTTGGCTCCTGTAT
TAACACAGTAATACCTCGCTTCTCTGTGCATTTAGCTGGGAATGTTCCCGCTATGGTGACCGGA
ATAAAGTTATTAACATGAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_476438	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB27554	(Get FASTA)	NCBI Sequence Viewer
	AAH88119	(Get FASTA)	NCBI Sequence Viewer
	EDL81202	(Get FASTA)	NCBI Sequence Viewer
	P63025	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_476438 ⟸ NM_057097
- UniProtKB:	Q64271 (UniProtKB/Swiss-Prot), P63025 (UniProtKB/Swiss-Prot), A6IUF1 (UniProtKB/TrEMBL), A0A8L2QPJ9 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSTGVPSGSSAATGSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQF ETSAAKLKRKYWWKNCKMWAIGISVLVIIVIIIIVWCVS hide sequence

Ensembl Acc Id:

ENSRNOP00000048364 ⟸ ENSRNOT00000051554

Ensembl Acc Id:

ENSRNOP00000082314 ⟸ ENSRNOT00000108568

Ensembl Acc Id:

ENSRNOP00000083016 ⟸ ENSRNOT00000110400

Ensembl Acc Id:

ENSRNOP00000103069 ⟸ ENSRNOT00000146635

Protein Domains

v-SNARE coiled-coil homology

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P63025-F1-model_v2	AlphaFold	P63025	1-103	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694288

Promoter ID:

EPDNEW_R4813

Type:

initiation region

Name:

Vamp3_1

Description:

vesicle-associated membrane protein 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	168,136,646 - 168,136,706	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61880	AgrOrtholog
BioCyc Gene	G2FUF-39043	BioCyc
Ensembl Genes	ENSRNOG00000030055	Ensembl
Gene3D-CATH	1.20.5.110	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7366421	IMAGE-MGC_LOAD
InterPro	Synaptobrevin	UniProtKB/Swiss-Prot
	Synaptobrevin/VAMP	UniProtKB/Swiss-Prot
	V_SNARE_CC	UniProtKB/Swiss-Prot
KEGG Report	rno:29528	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:108618	IMAGE-MGC_LOAD
NCBI Gene	29528	ENTREZGENE
PANTHER	PTHR45701	UniProtKB/Swiss-Prot
Pfam	Synaptobrevin	UniProtKB/Swiss-Prot
PhenoGen	Vamp3	PhenoGen
PIRSF	Synaptobrevin_euk	UniProtKB/Swiss-Prot
PRINTS	SYNAPTOBREVN	UniProtKB/Swiss-Prot
PROSITE	SYNAPTOBREVIN	UniProtKB/Swiss-Prot
	V_SNARE	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000030055	RatGTEx
Superfamily-SCOP	SNARE fusion complex	UniProtKB/Swiss-Prot
UniProt	A0A8I5ZZ29_RAT	UniProtKB/TrEMBL
	A0A8L2QPJ9	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0L2K2_RAT	UniProtKB/TrEMBL
	A6IUF1	ENTREZGENE, UniProtKB/TrEMBL
	P63025	ENTREZGENE
	Q64271	ENTREZGENE
	VAMP3_RAT	UniProtKB/Swiss-Prot
UniProt Secondary	Q64271	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Vamp3	vesicle-associated membrane protein 3			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in facial motor nucleus; expression is downregulated in facial nucleus following axotomy	727412
gene_process	may play a role in nerve regeneration	727412

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Send us a Message

RGD Manual Annotations

Imported Annotations - KEGG (archival)