Human Gene VAMP3 (ENST00000054666.11_4) from GENCODE V47lift37

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Description: vesicle associated membrane protein 3 (from RefSeq NM_004781.4)
Gencode Transcript: ENST00000054666.11_4
Gencode Gene: ENSG00000049245.13_8
Transcript (Including UTRs)
Position: hg19 chr1:7,831,356-7,841,492 Size: 10,137 Total Exon Count: 5 Strand: +
Coding Region
Position: hg19 chr1:7,831,444-7,839,705 Size: 8,262 Coding Exon Count: 5

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:7,831,356-7,841,492)			mRNA (may differ from genome)		Protein (100 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
Human Cortex Gene Expression	Malacards	MGI	OMIM	PubMed	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: Q6FGG2_HUMAN DESCRIPTION: SubName: Full=VAMP3 protein; SubName: Full=Vesicle-associated membrane protein 3 (Cellubrevin); SubName: Full=cDNA, FLJ92013, Homo sapiens vesicle-associated membrane protein 3 (cellubrevin)(VAMP3), mRNA; SIMILARITY: Contains 1 v-SNARE coiled-coil homology domain.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: VAMP3 Diseases sorted by gene-association score: tetanus (7), primary bacterial infectious disease (1)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C006780 bisphenol A C049325 1,2-dithiol-3-thione C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone C009505 4,4'-diaminodiphenylmethane D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D000082 Acetaminophen D000643 Ammonium Chloride D004054 Diethylstilbestrol D000431 Ethanol D005839 Gentamicins more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 75.97 RPKM in Brain - Spinal cord (cervical c-1) Total median expression: 1863.47 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-16.00	88	-0.182	Picture	PostScript	Text
3' UTR	-467.80	1787	-0.262	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR001388 - Synaptobrevin
IPR016444 - Synaptobrevin_met/fun

Pfam Domains:
PF00957 - Synaptobrevin

SCOP Domains:
58038 - SNARE fusion complex
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on Q6FGG2


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000149 SNARE binding GO:0017075 syntaxin-1 binding Biological Process: GO:0001921 positive regulation of receptor recycling GO:0016192 vesicle-mediated transport GO:0017156 calcium ion regulated exocytosis GO:0034446 substrate adhesion-dependent cell spreading GO:0035493 SNARE complex assembly GO:0043001 Golgi to plasma membrane protein transport GO:0065003 macromolecular complex assembly GO:0071346 cellular response to interferon-gamma Cellular Component: GO:0005829 cytosol GO:0005886 plasma membrane GO:0009986 cell surface GO:0016020 membrane GO:0016021 integral component of membrane GO:0016324 apical plasma membrane GO:0030141 secretory granule GO:0030665 clathrin-coated vesicle membrane GO:0031201 SNARE complex GO:0031410 cytoplasmic vesicle GO:0043229 intracellular organelle GO:0043231 intracellular membrane-bounded organelle GO:0045335 phagocytic vesicle GO:0048471 perinuclear region of cytoplasm GO:0055037 recycling endosome

Descriptions from all associated GenBank mRNAs


	BC005941 - Homo sapiens vesicle-associated membrane protein 3 (cellubrevin), mRNA (cDNA clone MGC:14563 IMAGE:4069433), complete cds. AK316558 - Homo sapiens cDNA, FLJ92013, Homo sapiens vesicle-associated membrane protein 3 (cellubrevin)(VAMP3), mRNA. BC007050 - Homo sapiens vesicle-associated membrane protein 3 (cellubrevin), mRNA (cDNA clone MGC:12463 IMAGE:3681914), complete cds. BC003570 - Homo sapiens vesicle-associated membrane protein 3 (cellubrevin), mRNA (cDNA clone MGC:2110 IMAGE:3544610), complete cds. U64520 - Homo sapiens synaptobrevin-3 mRNA, complete cds. AB528480 - Synthetic construct DNA, clone: pF1KE1064, Homo sapiens VAMP3 gene for vesicle-associated membrane protein 3, without stop codon, in Flexi system. CR542154 - Homo sapiens full open reading frame cDNA clone RZPDo834G1223D for gene VAMP3, vesicle-associated membrane protein 3 (cellubrevin); complete cds, without stopcodon. BT007327 - Homo sapiens vesicle-associated membrane protein 3 (cellubrevin) mRNA, complete cds. KJ905996 - Synthetic construct Homo sapiens clone ccsbBroadEn_15666 VAMP3 gene, encodes complete protein. KJ892751 - Synthetic construct Homo sapiens clone ccsbBroadEn_02145 VAMP3 gene, encodes complete protein. CR542145 - Homo sapiens full open reading frame cDNA clone RZPDo834E0523D for gene VAMP3, vesicle-associated membrane protein 3 (cellubrevin); complete cds, incl. stopcodon. JD153816 - Sequence 134840 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: ENST00000054666.1, ENST00000054666.10, ENST00000054666.2, ENST00000054666.3, ENST00000054666.4, ENST00000054666.5, ENST00000054666.6, ENST00000054666.7, ENST00000054666.8, ENST00000054666.9, hCG_21813 , NM_004781, Q6FGG2, Q6FGG2_HUMAN, uc317bzz.1, uc317bzz.2, VAMP3 UCSC ID: ENST00000054666.11_4 RefSeq Accession: NM_004781.4 Protein: Q6FGG2

Gene Model Information


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Methods, Credits, and Use Restrictions


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