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Gene : EDA9 A. thaliana

Gene ID  ? AT4G34200
Brief Description  D-3-phosphoglycerate dehydrogenase  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? embryo sac development arrest 9 (EDA9); FUNCTIONS IN: ATP binding; INVOLVED IN: megagametogenesis; LOCATED IN: mitochondrion, chloroplast, membrane; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: D-3-phosphoglycerate dehydrogenase (InterPro:IPR006236), D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (InterPro:IPR006139), D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (InterPro:IPR006140), D-3-phosphogylcerate Dehydrogenase (InterPro:IPR015508), Amino acid-binding ACT (InterPro:IPR002912), NAD(P)-binding domain (InterPro:IPR016040); BEST Arabidopsis thaliana protein match is: D-3-phosphoglycerate dehydrogenase (TAIR:AT3G19480.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Encodes a 3-phosphoglycerate dehydrogenase that is essential for embryo and pollen development.  Source: TAIR, Jun 30, 2015.
Name  ? embryo sac development arrest 9
  • synonyms:
  • phosphoglycerate dehydrogenase 1,
  • PGDH1

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3 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots. 24058165
Genetic and molecular evidence were provided for the essential role of EDA9 for embryo and pollen development. 24304635
PGDH1 is essential for Arabidopsis development. 24368794


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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
AT4G34200 0.5kb upstream 0.5kb upstream 3436   true Chr4: 16373731-16377166
AT4G34200 0.5kb upstream 0.5kb upstream 500   false Chr4: 16376667-16377166
AT4G34200 0.5kb downstream 0.5kb downstream 3436   true Chr4: 16373231-16376666
AT4G34200 0.5kb downstream 0.5kb downstream 500   false Chr4: 16373231-16373730
AT4G34200 1.0kb upstream 1.0kb upstream 3936   true Chr4: 16373731-16377666
AT4G34200 1.0kb upstream 1.0kb upstream 1000   false Chr4: 16376667-16377666
AT4G34200 1.0kb downstream 1.0kb downstream 3936   true Chr4: 16372731-16376666
AT4G34200 1.0kb downstream 1.0kb downstream 1000   false Chr4: 16372731-16373730
AT4G34200 3.0kb upstream 3.0kb upstream 5936   true Chr4: 16373731-16379666
AT4G34200 3.0kb upstream 3.0kb upstream 3000   false Chr4: 16376667-16379666
AT4G34200 3.0kb downstream 3.0kb downstream 5936   true Chr4: 16370731-16376666
AT4G34200 3.0kb downstream 3.0kb downstream 3000   false Chr4: 16370731-16373730


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4 Pathways

Data Source: KEGG

Identifier Name
01100 Metabolic pathways
01200 Carbon metabolism
01230 Biosynthesis of amino acids
00260 Glycine, serine and threonine metabolism

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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