Results 1 to 10 of about 780,008 (208)

Standardized annotation of translated open reading frames. [PDF]

Nat Biotechnol, 2022
Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes.
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S.   +34 more
europepmc   +9 more sources

Noise reduction by upstream open reading frames. [PDF]

Nat Plants, 2022
Gene expression is prone to burst production, making it a highly noisy process that requires additional controls. Upstream open reading frames (uORFs) are widely present in the 5′ leader sequences of 30–50% of eukaryotic messenger RNAs1–3.
Wu HW, Fajiculay E, Wu JF, Yan CS, Hsu CP, Wu SH.   +5 more
europepmc   +4 more sources

Classification and function of small open reading frames [PDF]

Nature Reviews Molecular Cell Biology, 2017
Small open reading frames (smORFs) of 100 codons or fewer are usually - if arbitrarily - excluded from proteome annotations. Despite this, the genomes of many metazoans, including humans, contain millions of smORFs, some of which fulfil key physiological
A Fatica, A Joliot, A Pauli, A Saghatelian, A Yates, AA Bazzini, AC Staudt, AR Carvunis, B Banfai, B Guo, B Lemaitre, B Szamecz, BA Moyers, BA Schulman, BR Nelson, C Fritsch, C Ghiglione, C Lee, C Palm, C Pegueroles, C Schlotterer, C Xie, CD Duncan, CR Loose, D Lauressergues, D Waxman, DL Vaux, DM Anderson, E Ladoukakis, EG Magny, F Ling, G Abrusan, G Baggerman, G D'Onofrio, G Weinmaster, GL Chew, GLG Miklos, GM Rubin, H Wang, I Ebina, I Kronja, J Alonso, J Crappe, J Ma, J Ruiz-Orera, J Zanet, JA Hoffmann, JA Reinhardt, JE Smith, JG Dunn, JI Pueyo, JI Pueyo, JI Pueyo, JI Pueyo, JL Aspden, JP Combier, JP Kastenmayer, Juan-Pablo Couso, K Hanada, K Hanyu-Nakamura, K Itoh, KA Brogden, KH Ching, L Fan, L Zhao, LA Kelley, M Graeff, M Guttman, M Guttman, M Hansen, M Kozak, M Wenzel, M Zasloff, MA Basrai, MA Mumtaz, MB Gerstein, MC Frith, MI Galindo, MJ Milligan, ML Billingsley, MM Kessler, MP Murphy, MR Hemm, NT Ingolia, NT Ingolia, O Jaillon, P Gawlin´ski, Pedro Patraquim, PJ Seo, Q Zhou, R Neme, RJ Sommer, S Djakovic, S van Heesch, S Yang, SA Slavoff, SA Slavoff, SC Chng, SD Mackowiak, SE Calvo, SJ Andrews, SW Jones, SW Pimplikar, T Derrien, TG Johnstone, V Paharkova, XQ Wang, Y Au, Z Ji, Z Li, Z Zhang   +110 more
core   +6 more sources

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq [PDF]

eLife, 2014
Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear.
Julie L Aspden, Ying Chen Eyre-Walker, Rose J Phillips, Unum Amin, Muhammad Ali S Mumtaz, Michele Brocard, Juan-Pablo Couso   +6 more
doaj   +5 more sources

Gene expression regulation by upstream open reading frames and human disease. [PDF]

PLoS Genetics, 2013
Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region.
Cristina Barbosa, Isabel Peixeiro, Luísa Romão   +2 more
doaj   +6 more sources

Identification of short open reading frames in plant genomes [PDF]

Frontiers in Plant Science, 2023
The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which ...
Yong Feng, Mengyun Jiang, Mengyun Jiang, Weichang Yu, Weichang Yu, Jiannan Zhou   +5 more
doaj   +2 more sources

ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files [PDF]

BMC Bioinformatics, 2002
Background Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins.
Sievert Volker, Hoffmann Steve, Büssow Konrad   +2 more
doaj   +2 more sources

Integrated workflow for discovery of microprotein-coding small open reading frames [PDF]

STAR Protocols, 2023
Summary: Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100–150 amino acids, are an emerging class of functional biomolecules.
Kevin Cao, Yasamin Hajy Heydary, Gregory Tong, Thomas Farid Martinez   +3 more
doaj   +2 more sources

Small open reading frames: a comparative genetics approach to validation [PDF]

BMC Genomics, 2023
Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the ...
Niyati Jain, Felix Richter, Ivan Adzhubei, Andrew J. Sharp, Bruce D. Gelb   +4 more
doaj   +2 more sources

A novel class of microRNA-recognition elements that function only within open reading frames. [PDF]

Nature Structural & Molecular Biology, 2018
MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level.
A Aizer, A Helwak, A Jakymiw, A Lal, AE Pasquinelli, AJ Giraldez, Alexander Dobin, AM Duursma, AR Buskirk, AR Quinlan, B Langmead, Bing Zhou, CJ Decker, CJ Shoemaker, CJ Woolstenhulme, CP Petersen, Dehe Wang, DP Bartel, DT Humphreys, E Huntzinger, EL Nostrand Van, GB Loeb, Guangqiao Liu, H Guo, HA Meijer, HO Iwakawa, I Behm-Ansmant, I Elcheva, J Hausser, J Liu, J Liu, JH Kim, Jie Zhou, JJ Forman, JP Broughton, K Seggerson, KA O’Donnell, Kai Zhang, L Wu, Ligang Wu, M Hafner, M Kouwenhove van, M Rehmsmeier, MD Robinson, MK Doma, ML Donnelly, N Rajewsky, NT Schirle, PA Maroney, Qian Zhao, R Ishimura, R Ishimura, R Parker, Ran Cao, RS Pillai, S Bagga, S Djuranovic, S Grosswendt, S Gu, S Jonas, S Nottrott, S Takagi, SN Bhattacharyya, SW Chi, SW Eichhorn, Timothy Nilsen, TT Tat, V Presnyak, W Filipowicz, Wen Ruan, X Adiconis, Xiang-Dong Fu, Xiaorong Zhang, Y Ishigaki, Y Liao, Y Tay, Y Wang, Y Xue, Y Zhao, Ya Zhao, Yan Qin, Yu Zhou, Yuanchao Xue, Z Cai, Zhiqiang Cai, Zonggui Chen   +85 more
core   +3 more sources