help  | faq  | software  | ARAPORT

Gene : RARE1 A. thaliana

Gene ID  ? AT5G13270
Brief Description  Pentatricopeptide repeat (PPR) superfamily protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? REQUIRED FOR ACCD RNA EDITING 1 (RARE1); CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT3G49170.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Encodes RARE1 (Required for accD RNA Editing 1), a trans-factor essential for C-to-U editing of the chloroplast accD transcript. RARE1 carries 15 PPR (pentatricopeptide repeat) motifs, an E/E and a DYW domain (C-terminal tripeptide).  Source: TAIR, Jun 30, 2015.
Name  ? REQUIRED FOR ACCD RNA EDITING 1

Locus History Displayer

Publication Counts Displayer

1 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Data show that the presence RIP1 (At3g15000.1) in a protein complex with chloroplast editing factor RARE1 (At5g13270.1) indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets. 22566615

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
AT5G13270 0.5kb upstream 0.5kb upstream 2854   true Chr5: 4246954-4249807
AT5G13270 0.5kb upstream 0.5kb upstream 500   false Chr5: 4249308-4249807
AT5G13270 0.5kb downstream 0.5kb downstream 2854   true Chr5: 4246454-4249307
AT5G13270 0.5kb downstream 0.5kb downstream 500   false Chr5: 4246454-4246953
AT5G13270 1.0kb upstream 1.0kb upstream 3354   true Chr5: 4246954-4250307
AT5G13270 1.0kb upstream 1.0kb upstream 1000   false Chr5: 4249308-4250307
AT5G13270 1.0kb downstream 1.0kb downstream 3354   true Chr5: 4245954-4249307
AT5G13270 1.0kb downstream 1.0kb downstream 1000   false Chr5: 4245954-4246953
AT5G13270 3.0kb upstream 3.0kb upstream 5354   true Chr5: 4246954-4252307
AT5G13270 3.0kb upstream 3.0kb upstream 3000   false Chr5: 4249308-4252307
AT5G13270 3.0kb downstream 3.0kb downstream 5354   true Chr5: 4243954-4249307
AT5G13270 3.0kb downstream 3.0kb downstream 3000   false Chr5: 4243954-4246953

Proteins

Protein Displayer


Function

Gene Ontology Displayer

0 Pathways

Data Source: KEGG

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

10 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 InterPro    
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
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139