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LETTER: A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
- Isabel Aznarez,
- Yoseph Barash,
- Ofer Shai,
- David He,
- Julian Zielenski,
- Lap-Chee Tsui,
- John Parkinson,
- Brendan J. Frey,
- Johanna M. Rommens,
- and Benjamin J. Blencowe
Genome Res. August 2008 18: 1247-1258; Published in Advance May 2, 2008, doi:10.1101/gr.073155.107
...sequences, SeedSearcher ( Barash et al. 2001 ; Fagnani et al. 2007 ) was employed. This algorithm searches for enrichment of motifs of variable length and composition in test sequences relative to control sequences. In order to exclude the 5′ splice site consensus sequence, searches were conducted at each...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...at cis-regulatory elements (Lago et al. 2021; Shen et al. 2021; Spiegel et al. 2021; Georgakopoulos-Soares et al. 2022a,d), including in promoters, enhancers, and CTCF binding sites, whereas in higher eukaryotes, they have also emerged in proximity to splice sites to modulate alternative splicing...
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RESOURCE: The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) Genome Res. October 15, 2004 14: 2121-2127; doi:10.1101/gr.2596504

...on the genomic sequence with canonical splice-site recognition was used. Within the ORF, all differences were identified as either synonymous or nonsynonymous by using the protein-coding sequence of the MGC clones. The differences, which correspond to known mRNA variations recorded in dbSNP v. 117 ( http...
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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
...this characteristic by measuring average conservation in introns on an individual nucleotide level across the seven species described above using the program phyloP (Pollard et al. 2010). We focused on the 23 nt adjacent to each splice site, because this length would still partition our smallest introns (∼40 nt...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
..., splice site variants, and deletions, are easily recognized yet only account for a limited part of the genetic variance for complex phenotypes, including production traits. It is increasingly apparent that most of the genetic variation for complex traits is owing to regulatory variants that act either...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
..., propensity to form local secondary structure, splice site strength scores, conservation scores, and nucleosome positioning scores (Supplemental Table S9A). This feature information was used to train a three-layer deep neural network (DNN) tasked with predicting whether an intron belonged in Group A, B, C...
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Method: TransMeta simultaneously assembles multisample RNA-seq reads
- Ting Yu,
- Xiaoyu Zhao,
- and Guojun Li
Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
...simulated data sets. Thus, the following additional tests were made based on data set S1. First, as is known, for the simulated data set, the ground truth was known with certainty. Therefore, we further ran HISAT2 via using the options ‐‐ss and ‐‐exon, which, respectively, provided the splice sites...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...-regulated differential expression was observed, indicating that TIPs influence host genes in both directions. Such influences may result from novel enhancers, transposases, alternative splice sites, or polyadenylation signals imbedded in TE insertions, some of which may be of adaptive significance or may contribute...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...for regulating the protein activity (Bhattacharyya et al. 2020). Moreover, all the s-exons defined by ThorAxe are conserved at least as far as amphibians. The smallest s-exon (25_1) contains only one column of alanines and corresponds to a well-documented internal splice site (Sloutsky and Stratton 2020...
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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
...-exons are highly conserved across vertebrates and mammals at the sequence and exon inclusion levels, respectively. Analysis of 7949 brain-expressed micro-exons revealed that constitutively spliced (CS) micro-exons possess strong genomic signatures predicted to facilitate splicing, including stronger splice-site...
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