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AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana

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Title AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana
 
Creator Singh, Ajeet
Zahra, Shafaque
Das, Durdam
Kumar, Shailesh
 
Subject Database tool
Arabidopsis thaliana
AtFusionDB
 
Description Accepted date: 29 November 2018
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.
Database URL: http://www.nipgr.res.in/AtFusionDB
The authors are thankful to the Department of Biotechnology (DBT)-
eLibrary Consortium, India, for providing access to e-resources. S.Z.
and A.S. are thankful to the Council of Scientific and Industrial
Research, India, for research fellowships. Authors are thankful to the
Distributed Information Sub-Centers of DBT at National Institute of
Plant Genome Research.
 
Date 2019-01-11T10:25:26Z
2019-01-11T10:25:26Z
2019
 
Type Article
 
Identifier Database, 2019: bay135
1758-0463
http://223.31.159.10:8080/jspui/handle/123456789/909
https://academic.oup.com/database/article/doi/10.1093/database/bay135/5277248#
https://doi.org/10.1093/database/bay135
 
Language en_US
 
Format application/pdf
 
Publisher Oxford University Press