help  | faq  | software  | ARAPORT

Gene : VAM3 A. thaliana

Gene ID  ? AT5G46860
Brief Description  Syntaxin/t-SNARE family protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? VACUOLAR MORPHOLOGY 3 (VAM3); FUNCTIONS IN: SNAP receptor activity; INVOLVED IN: in 7 processes; LOCATED IN: late endosome, trans-Golgi network transport vesicle, plant-type vacuole membrane, vacuole, plant-type vacuole; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Target SNARE coiled-coil domain (InterPro:IPR000727), t-SNARE (InterPro:IPR010989), Syntaxin/epimorphin, conserved site (InterPro:IPR006012), Syntaxin, N-terminal (InterPro:IPR006011); BEST Arabidopsis thaliana protein match is: syntaxin of plants 23 (TAIR:AT4G17730.2).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Syntaxin-related protein required for vacuolar assembly. A member of t-SNARE superfamily, homologous to yest Vam3p. Localized in the vacuolar membranes. The protein has a heptad repeat structure (residues164–220) in which hydrophobic amino acid residues appear at seven amino acid intervals. Such regions have a high potential to form an amphiphilic a-helix, intriguing for the intermolecular interactions by forming coiled-coil structure. AtVam3p has a highly hydrophobic segment at its C terminus thus implicating it to be a membrane protein while the rest of the sequence is hydrophilic.  Source: TAIR, Jun 30, 2015.
  • synonyms:
  • ATVAM3,
  • SYP22,
  • SGR3,
  • ATSYP22

Locus History Displayer

Publication Counts Displayer

8 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
has a plant-specific function in development of myrosin cells 16306062
SYP22 is suppressed by VAMP727, and is associated with the fusion between the prevacuolar compartment and the vacuole. 18984676
VAM3 is involved in the formation of the vascular network in leaves, and is required for the proper expression pattern of PIN1. Deficiency causes abnormal distribution of auxin in leaf primordia. 19493960
The functions of VAM3/SYP22 and PEP12/SYP21 are redundant and interchangeable. 21105932
SYP21, SYP22 and SYP23 function redundantly in vacuolar protein transport, vein patterning, myrosin cell differentiation and plant growth. 21143674
The frequency of bulbs is affected in the three sgr mutants sgr2, sgr3 and sgr4/zig. 21645145
Vam3 is more concentrated than GFP-AtRab75 in the vacuolar bulb membrane. 22105033
vacuolar and/or endocytic trafficking is involved in the FLC regulation of flowering time in A. thaliana 22848750


Sequence Feature Displayer

Gene Structure Displayer

J Browse Displayer

Overlapping Features Displayer

12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT5G46860 0.5kb upstream 0.5kb upstream 2590   true Chr5: 19012021-19014610
AT5G46860 0.5kb upstream 0.5kb upstream 500   false Chr5: 19014111-19014610
AT5G46860 0.5kb downstream 0.5kb downstream 2590   true Chr5: 19011521-19014110
AT5G46860 0.5kb downstream 0.5kb downstream 500   false Chr5: 19011521-19012020
AT5G46860 1.0kb upstream 1.0kb upstream 3090   true Chr5: 19012021-19015110
AT5G46860 1.0kb upstream 1.0kb upstream 1000   false Chr5: 19014111-19015110
AT5G46860 1.0kb downstream 1.0kb downstream 3090   true Chr5: 19011021-19014110
AT5G46860 1.0kb downstream 1.0kb downstream 1000   false Chr5: 19011021-19012020
AT5G46860 3.0kb upstream 3.0kb upstream 5090   true Chr5: 19012021-19017110
AT5G46860 3.0kb upstream 3.0kb upstream 3000   false Chr5: 19014111-19017110
AT5G46860 3.0kb downstream 3.0kb downstream 5090   true Chr5: 19009021-19014110
AT5G46860 3.0kb downstream 3.0kb downstream 3000   false Chr5: 19009021-19012020


Protein Displayer


Gene Ontology Displayer

2 Pathways

Data Source: KEGG

Identifier Name
04145 Phagosome
04130 SNARE interactions in vesicular transport

Gene --> Ontology term

Gene --> Pathways


Plant Ontology Displayer

Bar Efp Browser Displayer

Array Expression

RNA-seq Expression


Save / Export






Cytoscape Network Displayer


Homologue Displayer

Phytomine Ortholog Displayer


Alelle Table Displayer

Stock Gene Table Displayer



12 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from GOC GO annotations assigned by the GO Consortium 8/01/2016
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
KEGG pathways data set Wiring diagrams of molecular interactions, reactions, and relations 79.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139