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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
..., apparent differences to published assay results could be ascribed to differences in the experimental designs. For BRCA1 c.442-3T>G, the SeqSplice construct-based quantitative analysis showed complete impact on splicing compared with the reported incomplete impact (splice class 2S) from RT-PCR-based...
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Research: HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
- Jonathan M. Howard,
- Hai Lin,
- Andrew J. Wallace,
- Garam Kim,
- Jolene M. Draper,
- Maximilian Haeussler,
- Sol Katzman,
- Masoud Toloue,
- Yunlong Liu,
- and Jeremy R. Sanford
Genome Res. May 2018 28: 689-698; Published in Advance April 12, 2018, doi:10.1101/gr.229062.117
...DNA 1000 assay of RT-PCR products from SRSF6 splicing construct transfections. (I) Bar graph depicting mean exon inclusion for SRSF6 splicing reporters quantified using an Agilent 2100 Bioanalyzer with standard deviation bars. (*) P < 0.05.View this table: In this window In a new window Table 2...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...ORF), which encompasses all of the above definitions. Specifically, a nORF is any ORF that can encode a not-yet-classified transcript or protein product, or an isoform of one, with no bounds on the number of codons, location, number of ORFs per transcript, or start codon. Although nORFs may appear by chance...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...and the disorder, as well as the specificity of the phenotype. The relationship between our PPVs and the proportion of clinical diagnoses in each class of near-splice mutation was assessed using Pearson's product-moment correlation using the cor.test function in R (version 3.4.4) (R Core Team 2018).The proportion...
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Method: ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
- Riccardo Sangermano,
- Mubeen Khan,
- Stéphanie S. Cornelis,
- Valerie Richelle,
- Silvia Albert,
- Alejandro Garanto,
- Duaa Elmelik,
- Raheel Qamar,
- Dorien Lugtenberg,
- L. Ingeborgh van den Born,
- Rob W.J. Collin,
- and Frans P.M. Cremers
Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
..., and the mutant construct showed normal RNA product in addition to the exon 40 skipping product (Fig. 1B), as expected for a moderately severe variant.View larger version: In this window In a new window Figure 1. Large minigene enables accurate RNA analysis of the ABCA4 noncanonical splice site variant c.5714+5G...
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Method: The dynamic landscape of fission yeast meiosis alternative-splice isoforms
- Zheng Kuang,
- Jef D. Boeke,
- and Stefan Canzar
Genome Res. January 2017 27: 145-156; Published in Advance November 17, 2016, doi:10.1101/gr.208041.116
...distinct functional proteins from the same gene. On the contrary, a product of aberrant splicing is not responsible for generating functional proteins. Therefore, we performed systematic prediction of protein sequences from all isoforms detected in our study (Supplemental Table S10). Translation prediction...
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Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
- Steffen Erkelenz,
- Stephan Theiss,
- Wolfgang Kaisers,
- Johannes Ptok,
- Lara Walotka,
- Lisa Müller,
- Frank Hillebrand,
- Anna-Lena Brillen,
- Michael Sladek,
- and Heiner Schaal
Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
...). In order to identify the accurate splicing position with single nucleotide precision, we extracted the PCR products from the gel and sequenced them (Fig. 2C; Supplemental Fig. S1).View larger version: In this window In a new window Figure 2. Noncanonical 5′ss exhibit a greater enhancer dependency than...
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Research: U2AF1 mutations alter splice site recognition in hematological malignancies
- Janine O. Ilagan,
- Aravind Ramakrishnan,
- Brian Hayes,
- Michele E. Murphy,
- Ahmad S. Zebari,
- Philip Bradley,
- and Robert K. Bradley
Genome Res. January 2015 25: 14-26; Published in Advance September 29, 2014, doi:10.1101/gr.181016.114
...cells expressing WT or Q157R U2AF1 (bottom). (C ) Schematic of AdML pre-mRNA substrate used for in vitro splicing (top) and in vitro splicing of AdML substrate incubated with nuclear extract fromK562 cells expressingWT or S34YU2AF1 (bottom). Percentages are the fraction of second step products (splicedm...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...RNA isoform 31 choice. Finally, splicing of newly synthesized transcripts appears to occur in a binary 32 manner, largely happening either fully on both sides of 47,163 exons or not at all. These 33 data sets generated as part of the ENCODE Project illustrate the intricate and 34 coordinated regulation of RNA...
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Methods: A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
- Aaron E. Tenney,
- Jia Qian Wu,
- Laura Langton,
- Paul Klueh,
- Ralph Quatrano,
- and Michael R. Brent
Genome Res. February 2007 17: 212-218; Published in Advance January 8, 2007, doi:10.1101/gr.5661407
...A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices Aaron E. Tenney 1 , 4 , Jia Qian Wu 2 , 4 , Laura Langton 1 , Paul Klueh 3 , Ralph Quatrano...

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