ArticleBiology direct2007
Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach.
Article in Biology direct, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics.Database : the journal of biological databases and curation · 2016Article
- Improving mRNA 5' coding sequence determination in the mouse genome.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Article
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9 authors.
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Abstract
backgroundAll standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence completeness in the model organism Danio rerio (zebrafish).
resultsWe implemented a novel automated approach (5'_ORF_Extender) that systematically compares available expressed sequence tags (ESTs) with all the zebrafish experimentally determined mRNA sequences, identifies additional sequence stretches at 5' region and scans for the presence of all conditions needed to define a new, extended putative ORF. Our software was able to identify 285 (3.3%) mRNAs with putatively incomplete ORFs at 5' region and, in three example cases selected (selt1a, unc119.2, nppa), the extended coding region at 5' end was cloned by reverse transcription-polymerase chain reaction (RT-PCR).
conclusionThe implemented method, which could also be useful for the analysis of other genomes, allowed us to describe the relevance of the "5' end mRNA artifact" problem for genomic annotation and functional genomic experiment design in zebrafish.
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