help  | faq  | software  | ARAPORT

Gene : VGDH1 A. thaliana

Gene ID  ? AT2G47030
Brief Description  Plant invertase/pectin methylesterase inhibitor superfamily  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? VGDH1; FUNCTIONS IN: enzyme inhibitor activity, pectinesterase activity; INVOLVED IN: cell wall modification; LOCATED IN: endomembrane system, cell wall, plant-type cell wall; EXPRESSED IN: male gametophyte, flower, pollen tube; CONTAINS InterPro DOMAIN/s: Pectinesterase, active site (InterPro:IPR018040), Pectin lyase fold/virulence factor (InterPro:IPR011050), Pectinesterase, catalytic (InterPro:IPR000070), Pectinesterase inhibitor (InterPro:IPR006501), Pectin lyase fold (InterPro:IPR012334); BEST Arabidopsis thaliana protein match is: Plant invertase/pectin methylesterase inhibitor superfamily (TAIR:AT2G47040.1).  Source: TAIR, Jun 30, 2015.

Locus History Displayer

Publication Counts Displayer

0 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Genomics

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
AT2G47030 0.5kb upstream 0.5kb upstream 2851   true Chr2: 19324134-19326984
AT2G47030 0.5kb upstream 0.5kb upstream 500   false Chr2: 19326485-19326984
AT2G47030 0.5kb downstream 0.5kb downstream 2851   true Chr2: 19323634-19326484
AT2G47030 0.5kb downstream 0.5kb downstream 500   false Chr2: 19323634-19324133
AT2G47030 1.0kb upstream 1.0kb upstream 3351   true Chr2: 19324134-19327484
AT2G47030 1.0kb upstream 1.0kb upstream 1000   false Chr2: 19326485-19327484
AT2G47030 1.0kb downstream 1.0kb downstream 3351   true Chr2: 19323134-19326484
AT2G47030 1.0kb downstream 1.0kb downstream 1000   false Chr2: 19323134-19324133
AT2G47030 3.0kb upstream 3.0kb upstream 5351   true Chr2: 19324134-19329484
AT2G47030 3.0kb upstream 3.0kb upstream 3000   false Chr2: 19326485-19329484
AT2G47030 3.0kb downstream 3.0kb downstream 5351   true Chr2: 19321134-19326484
AT2G47030 3.0kb downstream 3.0kb downstream 3000   false Chr2: 19321134-19324133

Proteins

Protein Displayer


Function

Gene Ontology Displayer

3 Pathways

Data Source: KEGG

Identifier Name
01100 Metabolic pathways
00500 Starch and sucrose metabolism
00040 Pentose and glucuronate interconversions

Gene --> Ontology term

Gene --> Pathways


Expression

Plant Ontology Displayer

Bar Efp Browser Displayer

Array Expression

RNA-seq Expression

Co-expression

Save / Export

 

 

 

 



Interactions

Cytoscape Network Displayer


Homology

Homologue Displayer

Phytomine Ortholog Displayer


Stocks

Alelle Table Displayer

Stock Gene Table Displayer


 

Other

11 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 UniProt GO annotations assigned by UniProt 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
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