Computational protocol: REL2, A Gene Encoding An Unknown Function Protein which Contains DUF630 and DUF632 Domains Controls Leaf Rolling in Rice

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Protocol publication

[…] The full-length amino acid sequence of REL2 was downloaded from National Center for Biotechnology Information (NCBI) and its more than 50Ā % similarity protein sequences were obtained through a search of NCBI non-redundant protein sequences database (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The alignment of amino acid sequences was carried out by using ClustalX2.0 (Jeanmougin et al. ). A neighbor-joining tree was generated by MEGA5.1 software by the bootstrap method with 1,000 replicates (Tamura et al. ). [...] To understand the possible functions of candidate genes, the annotation of candidate genes had been referring to the rice GRAMENE database (http://www.gramene.org) and the Rice Annotation Project Database (http://rapdb.dna.affrc.go.jp/viewer/gbrowse/build4/). Furthermore, six pairs of primers were synthesized to amplify the whole gene sequences of Os10g0562100, Os10g0562200, Os10g0562500, Os10g0562550, Os10g0562600 and Os10g0562700 (Additional file : Table S2). Specific DNA fragments amplified by PCR from genomic DNA of WT and rel2 were cloned into pMD19-T vector and then sequenced by Invitrogen Biotechnology Co., Ltd (Shanghai, China). To determine the mutant sites, the specific sequences were used to do a BLAST against the whole genome sequences Nipponbare (http://blast.ncbi.nlm.nih.gov/). […]

Pipeline specifications

Software tools Clustal W, MEGA, GBrowse
Databases Gramene RAP-DB
Applications Phylogenetics, WGS analysis
Organisms Oryza sativa
Chemicals Nucleotides