PUBLICATION

Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach

Authors
Frabetti, F., Casadei, R., Lenzi, L., Canaider, S., Vitale, L., Facchin, F., Carinci, P., Zannotti, M., and Strippoli, P.
ID
ZDB-PUB-071129-12
Date
2007
Source
Biology Direct   2(1): 34 (Journal)
Registered Authors
Casadei, Raffaella, Frabetti, Flavia
Keywords
none
MeSH Terms
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Cloning, Molecular
  • Cluster Analysis
  • Computational Biology
  • DNA, Complementary/genetics
  • Databases, Factual
  • Expressed Sequence Tags*
  • Molecular Sequence Data
  • Open Reading Frames/genetics*
  • Phylogeny
  • RNA, Messenger/genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Software
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics
PubMed
18042283 Full text @ Biol. Direct
Abstract
BACKGROUND: All 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). Result: We 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). CONCLUSIONS: The 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. Open peer review This article was reviewed by Alexey V. Kochetov (nominated by Mikhail Gelfand), Shamil Sunyaev, and Gaspar Jekely. For the full reviews, please go to the Reviewers' Comments section.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping