Abstract
Fusion transcripts are chimeric RNAs generated as a result of fusion either at DNA or RNA level. These novel transcripts have been extensively studied in the case of human cancers but still remain underexamined in plants. In this study, we introduce the first plant-specific database of fusion transcripts named AtFusionDB (http://www.nipgr.res.in/AtFusionDB). This is a comprehensive database that contains the detailed information about fusion transcripts identified in model plant Arabidopsis thaliana. A total of 82 969 fusion transcript entries generated from 17 181 different genes of A. thaliana are available in this database. Apart from the basic information consisting of the Ensembl gene names, official gene name, tissue type, EricScore, fusion type, AtFusionDB ID and sample ID (e.g. Sequence Read Archive ID), additional information like UniProt, gene coordinates (together with the function of parental genes), junction sequence, expression level of both parent genes and fusion transcript may be of high utility to the user. Two different types of search modules viz. ‘Simple Search’ and ‘Advanced Search’ in addition to the ‘Browse’ option with data download facility are provided in this database. Three different modules for mapping and alignment of the query sequences viz. BLASTN, SW Align and Mapping are incorporated in AtFusionDB. This database is a head start for exploring the complex and unexplored domain of gene/transcript fusion in plants.
Highlights
The origin and evolution of new genes are the constant sources of evolutionary renovation and adaptation
This can be accomplished by translocation of the original genes at the DNA level or post-transcriptionally during splicing events, and it has been documented in diverse life forms [4]
Intra-chromosomal fusion transcripts are generated by fusion of genes or transcripts coming from the same chromosome while interchromosomal chimeric transcripts are formed as a result of gene or transcript fusion from different chromosomes [13]
Summary
The origin and evolution of new genes are the constant sources of evolutionary renovation and adaptation. We have developed a database named AtFusionDB which is the plantexclusive knowledge base for fusion transcripts predicted in the model plant Arabidopsis thaliana (the thale cress or mouse-ear cress). The FASTQ files of paired-end RNA-Seq run obtained from the previous step were given as an input to ‘EricScriptPlants’ (https://github.com/asherkhb/EricScript-Plants) for the identification of fusion transcripts in A. thaliana.
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