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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
...either by affecting post-transcriptional regulation or by regulating protein–protein interactions through changes in protein tertiary structure.ResultsDiscovery of micro-exons and quantification of their usageA total of 12,835 Ensembl-annotated internal micro-exons were identified in protein-coding genes...
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Resource: Genome-wide discovery of human splicing branchpoints
- Tim R. Mercer,
- Michael B. Clark,
- Stacey B. Andersen,
- Marion E. Brunck,
- Wilfried Haerty,
- Joanna Crawford,
- Ryan J. Taft,
- Lars K. Nielsen,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
...identification can also lend support to the inclusion of associated exons and exon variants presently absent fromcomprehensive gene catalogs such asGENCODE (Harrow et al. 2012). Strict filtering identified a group of 16 exons, including a conserved 21-nt micro-exon in theMAST2 gene (Supplemental Fig. 4F...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium; 7Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium; 8Department of Pharmaceutics, Ghent University, Ghent 9000, Belgium; 9Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud...
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Research: Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts
- Ricardo DeMarco,
- William Mathieson,
- Sophia J. Manuel,
- Gary P. Dillon,
- Rachel S. Curwen,
- Peter D. Ashton,
- Alasdair C. Ivens,
- Matthew Berriman,
- Sergio Verjovski-Almeida,
- and R. Alan Wilson
Genome Res. August 2010 20: 1112-1121; Published in Advance July 6, 2010, doi:10.1101/gr.100099.109
...hits only for nine MEG families among S. japonicum ESTs and 11 MEG families among S. haematobium ESTs. Further Figure 1. Exon size distribution in S. mansoni micro-exon genes. (A) Histogram of the symmetrical internal exon size distribution. (B) Histogram of asymmetrical internal exon and flanking exon...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
..., USA; 3Department of Computer and Information Science, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated...
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RESOURCE: Genome-wide assembly and analysis of alternative transcripts in mouse
- Alexei A. Sharov,
- Dawood B. Dudekula,
- and Minoru S.H. Ko
Genome Res. May 2005 15: 748-754; doi:10.1101/gr.3269805
...discovery of internal micro-exons. Genome Res. 13 : 1216 –1221. ↵ Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002 . Initial sequencing and comparative analysis of the mouse . Nature 420 : 520 –562...
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RESOURCE: EAnnot: A genome annotation tool using experimental evidence
- Li Ding,
- Aniko Sabo,
- Nicolas Berkowicz,
- Rekha R. Meyer,
- Yoram Shotland,
- Mark R. Johnson,
- Kymberlie H. Pepin,
- Richard K. Wilson,
- and John Spieth
Genome Res. December 2004 14: 2503-2509; doi:10.1101/gr.3152604
...perspective. Genome Res. 14 : 280 -286. ↵ Volfovsky, N., Haas, B.J., and Salzberg, S.L. 2003 . Computational discovery of internal micro-exons. Genome Res. 13 : 1216 -1221. ↵ Walsh, S., Anderson, M., and Cartinhour, S.W. 1998 . ACEDB: A database for information. Meth. Biochem. Anal. 39 : 299 -318. ↵ Zavolan...

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