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Citation
Ladoukakis, E., Pereira, V., Magny, E.G., Eyre-Walker, A., Couso, J.P. (2011). Hundreds of putatively functional small open reading frames in Drosophila.  Genome Biol. 12(11): R118.
FlyBase ID
FBrf0218190
Publication Type
Research paper
Abstract

The relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization.Using bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data.The combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist.

PubMed ID
PubMed Central ID
PMC3334604 (PMC) (EuropePMC)
Related Publication(s)
FlyBase analysis

Analysis of smORFs identified by Ladoukakis et al., 2011.
FlyBase Genome Annotators, 2014, Analysis of smORFs identified by Ladoukakis et al., 2011. [FBrf0226485]

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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Biol.
    Title
    Genome Biology
    Publication Year
    2000-
    ISBN/ISSN
    1474-7596 1474-760X
    Data From Reference