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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...author: fesigor@gmail.comAbstractGenomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been...
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COMMENTARY: Small open reading frames: Not so small anymore
- Richelle Sopko and
- Brenda Andrews
Genome Res. March 2006 16: 314-315; doi:10.1101/gr.4976706
.... 98 : 4569 –4574. ↵ Kastenmayer, J.P., Ni, L., Chu, A., Kitchen, L.E., Au, W.-C., Yang, H., Carter, C.D., Wheeler, D., Davis, R., Boeke, J.D., et al. 2006 . Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res. (this issue). ↵ Kessler, M.M., Zeng, Q., Hogan...
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LETTER: A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
- Kousuke Hanada,
- Xu Zhang,
- Justin O. Borevitz,
- Wen-Hsiung Li,
- and Shin-Han Shiu
Genome Res. May 2007 17: 632-640; Published in Advance March 29, 2007, doi:10.1101/gr.5836207
...and tiling array studies have revealed the presence of many unannotated genes. For protein coding genes, small coding sequences may not be identified by gene finders because of the conservative nature of prediction algorithms. In this study, we identified small open reading frames (sORFs) with high coding...
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Method: Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
- Xiaohan Yang,
- Timothy J. Tschaplinski,
- Gregory B. Hurst,
- Sara Jawdy,
- Paul E. Abraham,
- Patricia K. Lankford,
- Rachel M. Adams,
- Manesh B. Shah,
- Robert L. Hettich,
- Erika Lindquist,
- Udaya C. Kalluri,
- Lee E. Gunter,
- Christa Pennacchio,
- and Gerald A. Tuskan
Genome Res. April 2011 21: 634-641; Published in Advance March 2, 2011, doi:10.1101/gr.109280.110
...–4880. Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, et al. 2006. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.Genome Res 16: 365–373. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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LETTER: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
- Besma Ben Amor,
- Sonia Wirth,
- Francisco Merchan,
- Philippe Laporte,
- Yves d’Aubenton-Carafa,
- Judith Hirsch,
- Alexis Maizel,
- Allison Mallory,
- Antoine Lucas,
- Jean Marc Deragon,
- Herve Vaucheret,
- Claude Thermes,
- and Martin Crespi
Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
...RNAs. This heterogeneous class of transcripts generally does not contain any long open reading frame (ORF) (e.g., no ORF coding more than 70 amino acids). Even though some of these genes may encode oligopeptides, it has been shown that their RNA moiety plays a critical role in their function. In order to achieve...

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