Genome-scale analysis of human mRNA 5' coding sequences based on expressed sequence tag (EST) database.
The "5' end mRNA artifact" issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5' end sequence. We performed a systematic identification of coding regions at the 5' end of all human known mRNAs, using an automated expressed sequence tag (EST)-based approach. Following parsing of more than 7 million BLAT alignments, we found 477 human loci, out of 18,665 analyzed, in which an extension of the mRNA 5' coding region was identified. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 cDNAs, and the consequences for the functional studies of these loci are discussed. We also generated a list of 20,775 human mRNAs where the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5' in the current form.
Center for Research in Molecular Genetics Fondazione CARISBO, Department of Histology, Embryology and Applied Biology, University of Bologna, via Belmeloro 8, 40126 Bologna, Italy.
Raffaella
R
Casadei
Allison
A
Piovesan
Lorenza
L
Vitale
Federica
F
Facchin
Maria Chiara
MC
Pelleri
Silvia
S
Canaider
Eva
E
Bianconi
Flavia
F
Frabetti
Pierluigi
P
Strippoli
D020121:5' Untranslated Regions / Q000235:genetics*; D000595:Amino Acid Sequence; D003001:Cloning, Molecular; D018387:Codon, Initiator; D019295:Computational Biology; D018076:DNA, Complementary; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D056726:Genetic Association Studies / Q000379:methods*; D056426:Genetic Loci; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D020121:5' Untranslated Regions; D018387:Codon, Initiator; D018076:DNA, Complementary; D012333:RNA, Messenger