Searching journal content for articles similar to Pal et al. 21 (8): 1260.

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  1. Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
    • Yang I. Li,
    • Luis Sanchez-Pulido,
    • Wilfried Haerty,
    • and Chris P. Ponting
    Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
    ...to better understand whether and how they might affect the structure and function of a protein. We speculated that alternatively spliced micro-exons, much like longer AS exons, could generate multiple protein isoforms with distinct functions. This hypothesis is supported by the strong bias for micro...
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  2. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    .... The vector was transfected into HeLa cells, and extracted RNA was amplified using the primers indicated by arrows in a reverse-transcription polymerase chain reaction (RT-PCR) assay. (F) RT-PCR products of minigene assay for RYR3 pseudoexon (PE). Here, 284- and 208-bp transcripts were generated from...
  3. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
  4. ARTICLE: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
    • Piero Carninci,
    • Kazunori Waki,
    • Toshiyuki Shiraki,
    • Hideaki Konno,
    • Kazuhiro Shibata,
    • Masayoshi Itoh,
    • Katsunori Aizawa,
    • Takahiro Arakawa,
    • Yoshiyuki Ishii,
    • Daisuke Sasaki,
    • Hidemasa Bono,
    • Shinji Kondo,
    • Yuichi Sugahara,
    • Rintaro Saito,
    • Naoki Osato,
    • Shiro Fukuda,
    • Kenjiro Sato,
    • Akira Watahiki,
    • Tomoko Hirozane-Kishikawa,
    • Mari Nakamura,
    • Yuko Shibata,
    • Ayako Yasunishi,
    • Noriko Kikuchi,
    • Atsushi Yoshiki,
    • Moriaki Kusakabe,
    • Stefano Gustincich,
    • Kirk Beisel,
    • William Pavan,
    • Vassilis Aidinis,
    • Akira Nakagawara,
    • William A. Held,
    • Hiroo Iwata,
    • Tomohiro Kono,
    • Hiromitsu Nakauchi,
    • Paul Lyons,
    • Christine Wells,
    • David A. Hume,
    • Michela Fagiolini,
    • Takao K. Hensch,
    • Michelle Brinkmeier,
    • Sally Camper,
    • Junji Hirota,
    • Peter Mombaerts,
    • Masami Muramatsu,
    • Yasushi Okazaki,
    • Jun Kawai,
    • and Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703
    ...reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC...
  5. Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
    • Alla Mikheenko,
    • Andrey D. Prjibelski,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
    ...than read quality alone. We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.Long-read sequencing is being increasingly used in transcriptomics, particularly for barcoded unique molecules (Gupta et...
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  6. Research: Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
    • Pedro Miura,
    • Sol Shenker,
    • Celia Andreu-Agullo,
    • Jakub O. Westholm,
    • and Eric C. Lai
    Genome Res. May 2013 23: 812-825; Published in Advance March 21, 2013, doi:10.1101/gr.146886.112
    ...long intergenic noncoding (lincRNAs) from loci downstream from protein-coding genes. Our experimental tests failed to validate specific accumulation of lincRNA transcripts, and instead revealed strongly distal 3′ UTRs generated by alternative cleavage and polyadenylation (APA). With this perspective...
  7. Research: Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing
    • Joshua A. Arribere and
    • Wendy V. Gilbert
    Genome Res. June 2013 23: 977-987; Published in Advance April 11, 2013, doi:10.1101/gr.150342.112
    ..., culminating in NMD of the transcript. Unlike previous approaches, our technique enabled observation of alternative TL variants for hundreds of genes and revealed significant differences in translation in genes with distinct TL isoforms. TL-seq and TATL-seq are useful tools for annotation and functional...
  8. Method: mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain
    • Paul Hammer,
    • Michaela S. Banck,
    • Ronny Amberg,
    • Cheng Wang,
    • Gabriele Petznick,
    • Shujun Luo,
    • Irina Khrebtukova,
    • Gary P. Schroth,
    • Peter Beyerlein,
    • and Andreas S. Beutler
    Genome Res. June 2010 20: 847-860; Published in Advance May 7, 2010, doi:10.1101/gr.101204.109
    ...requisite amounts of RNA, and a limited capacity to identify new transcripts or RNA splice sites. Given these limitations, it is unlikely that microarray analysis can reveal the full extent of transcriptome reprogramming underlying neurological disorders, such as chronic pain. Ultra-high-throughput RNA...
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  9. Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
    • Niccoló Tesi,
    • Alex Salazar,
    • Yaran Zhang,
    • Sven van der Lee,
    • Marc Hulsman,
    • Lydian Knoop,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Anne-Fleur Schneider,
    • Maartje Pennings,
    • Kristel Sleegers,
    • Erik-Jan Kamsteeg,
    • Marcel Reinders,
    • and Henne Holstege
    Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
    ....5-fold increased risk of Alzheimer's disease (AD) when the TR exceeds 5720 bp (On Behalf of the BELNEU Consortium et al. 2018; De Roeck et al. 2019).Traditionally, the evaluation of TR lengths and sequences has been challenging. Conventional methods, such as repeat-primed polymerase chain reaction (RP...
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