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index_V1.php
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<!DOCTYPE html>
<html>
<head>
<title>GeLoc</title>
<meta charset="utf-8">
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<option value="Nipponbare">Nipponbare</option>
<option value="Kitaake">Kitaake</option>
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Gene card
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<h1 class="display-2">Welcome to GeLoc</h1><br/>
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<div id="home_text">
<p>
Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containing receptor (LRR-CR) families: the LRR-Receptor-Like Kinase (LRR-RLK), LRR-Receptor-Like Protein (LRR-RLP) and Nucleotide-binding LRR Receptor (NLR).
</p>
<p>
We have proposed manually curated annotations of these genes for reference rice genomes: nipponbare <a href="https://rapdb.dna.affrc.go.jp/download/irgsp1.html">(IRGSP-01) </a> and kitaake <a href="https://phytozome-next.jgi.doe.gov/info/OsativaKitaake_v3_1"> (KitaakeX-v3.1)</a> japonica cultivars.
</p>
<p>
These annotations include genes tagged as non-canonical because they contain nonsense mutations, as opposed to canonical genes that contain all expected features to be functional (see Gottin et al. 2021 for further details).
</p>
<p>
Geloc provides convenient tools to visualised and download these annotation data.
</p>
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<p>Please cite:</p>
<div id="gene_card">
<p>
Gottin, C., Dievart, A., Summo, M., Droc, G., Périn, C., Ranwez, V. and Chantret, N. (2021), A New Comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice. The Plant Journal. Accepted Author Manuscript. https://doi.org/10.1111/tpj.15456
</p>
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<h3>Releases</h3><br/>
<p><strong>2021-05-03 - Latest</strong></p>
<p><strong>2021-01-22</strong> <a href="previous.php">Browse this release here</a></p>
</div>
<!-- download -->
<div id="download_section" class="home_content" style="display: none">
<h3>Download</h3><br/>
<p><strong>Files "Peptides" and "CDS":</strong></p>
<p>These files contain amino acid and nuclotide sequences for LRR-CR genes.
For genes experiencing frameshift, the one or two bases that cause the frameshift are avoided in order
to have nucleotide sequence that can be translated.
</p>
<p><strong>Files "cDNA":</strong></p>
<p>These files contain nucleotide sequences for the complete LRR-CR genes without intron.
In the case of genes experiencing frameshift, the sequences cannot be translated in comprehensive protein
sequences. For all other genes, the files "CDS" and "cDNA" retrieve the same nucleotide seqences.
</p>
<p><strong>Files "cDNA_wFrameshift": </strong></p>
<p>These files contain nucleotide sequences of non-canonical genes. In the case
of genes experiencing frameshift, the sequence is completed with one or two "!" characters at the position
of the frameshift in order to conserve the right reading frame (also used by V. Ranwez et al. for the
MACSE programs). The translation of these sequences will create amino acid sequences with frameshift
caracterised by an "X" character.
</p>
<p><strong>Nipponbare</strong></p>
<a href="./data_current/dl/Nipponbare_IDs.txt.zip" download="Nipponbare_IDs.txt.zip">Nipponbare_IDs.txt.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip</a><br/>
<br/>
<p><strong>Kitaake</strong></p>
<a href="./data_current/dl/Kitaake_IDs.txt.zip" download="Kitaake_IDs.txt.zip">Kitaake_IDs.txt.zip</a><br/>
<a href="./data_current/dl/ORYSJ_kitaake_LRR-CR__20210503.gff.zip" download="ORYSJ_kitaake_LRR-CR__20210503.gff.zip">ORYSJ_kitaake_LRR-CR__20210503.gff.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip</a><br/>
<br/>
<p><strong>Orthologous</strong></p>
<a href="./data_current/dl/Nip_Kit_ortho.txt.zip" download="Nip_Kit_ortho.txt.zip">Nip_Kit_ortho.txt.zip</a><br/>
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