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Article

In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides

IGFL, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
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Author to whom correspondence should be addressed.
Academic Editor: Krzysztof Jagla
Cells 2021, 10(11), 2983; https://doi.org/10.3390/cells10112983
Received: 13 September 2021 / Revised: 17 October 2021 / Accepted: 26 October 2021 / Published: 2 November 2021
(This article belongs to the Special Issue Drosophila: A Model for Genetic Research)
It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the Bithorax-complex (BX-C), which was one of the first genomic regions described to contain long non-coding RNAs in Drosophila. We showed that several altORFs could be predicted from coding and non-coding sequences of BX-C. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two Drosophila Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during Drosophila embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo. View Full-Text
Keywords: lncRNA; smORF; altORF; ELM; SLiM lncRNA; smORF; altORF; ELM; SLiM
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MDPI and ACS Style

Naville, M.; Merabet, S. In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides. Cells 2021, 10, 2983. https://doi.org/10.3390/cells10112983

AMA Style

Naville M, Merabet S. In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides. Cells. 2021; 10(11):2983. https://doi.org/10.3390/cells10112983

Chicago/Turabian Style

Naville, Magali, and Samir Merabet. 2021. "In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides" Cells 10, no. 11: 2983. https://doi.org/10.3390/cells10112983

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