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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...trapping assay, in which a query sequence is cloned into the middle of a 1.6 kb intron, to survey the human (see Fig. 1 for a schematic overview and example data). If the query sequence contains an autonomous exon, that exon (or more than one exon) will be included in the resulting spliced transcript. We...
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Method: A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
- Hengxing Lu,
- Jun Liu,
- Tao Feng,
- Zihang Guo,
- Yunjun Yin,
- Fei Gao,
- Gengsheng Cao,
- Xuguang Du,
- and Sen Wu
Genome Res. May 2021 31: 900-909; Published in Advance April 1, 2021, doi:10.1101/gr.271312.120
...entry site; (pA) polyadenylation signal. (B) Representative microscopic images of mESC clones after puromycin selection in HIT-trapping. Red arrows indicate apoptotic clone (top), GFP-negative surviving clone (middle), and GFP-positive surviving clone (bottom), respectively. Scale bar, 50 µm. (C) PCR...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...College, Portland, Oregon 97202, USA; 3Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA Corresponding author: dmetzger@zoology.ubc.caAbstractSex chromosome dosage compensation is a model to understand the coordinated evolution of transcription; however, the advanced...
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Letter: Exon-trapping mediated by the human retrotransposon SVA
- Dustin C. Hancks,
- Adam D. Ewing,
- Jesse E. Chen,
- Katsushi Tokunaga,
- and Haig H. Kazazian, Jr
Genome Res. November 2009 19: 1983-1991; Published in Advance July 27, 2009, doi:10.1101/gr.093153.109
...) in independent reactions to answer three questions: (1) are SVAs exonized (PKC For + 1R primers); (2) what 39 SS exist in SVA (PKC For + 2R); and (3) can we detect SVA gene-trapping (PKC For + 3R). PCR products were analyzed on a 2% agarose gel (Fig. 6B); bands were cloned and sequenced. Bands from the lane...
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REVIEW: Protocols for trapping internal and 3'-terminal exons.
- P E Nisson,
- A Ally,
- and P C Watkins
Genome Res. August 1994 4: S24-S39
....A. , Buckler. A.J. Church D.M., Stotler, C.J. Rutter, J.L. Murrell, J.R. Trofatter, J.A. and Buckler. A.J. 1994 . Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genet. 6 : 98 – 105 . 14.. Auch, D. , Reth. M. Auch, D. and Reth. M. 1990 . Exon trap cloning...
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RESOURCE: Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
- Gwenn M. Hansen,
- Diane C. Markesich,
- Michael B. Burnett,
- Qichao Zhu,
- Karen M. Dionne,
- Lizabeth J. Richter,
- Richard H. Finnell,
- Arthur T. Sands,
- Brian P. Zambrowicz,
- and Alejandro Abuin
Genome Res. October 2008 18: 1670-1679; Published in Advance September 17, 2008, doi:10.1101/gr.078352.108
...by the splice acceptor element within the trapping construct, or alternatively, by direct gene disruption as a result of insertion within an exon. Gene trapping is inherently amenable to high-throughput, cost-effective mutant clone production and mutation identification. A single gene trapping vector can...
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Resource: Phenotypic annotation of the mouse X chromosome
- Brian J. Cox,
- Marion Vollmer,
- Owen Tamplin,
- Mei Lu,
- Steffen Biechele,
- Marina Gertsenstein,
- Claude van Campenhout,
- Thomas Floss,
- Ralf Kühn,
- Wolfgang Wurst,
- Heiko Lickert,
- and Janet Rossant
Genome Res. August 2010 20: 1154-1164; Published in Advance June 14, 2010, doi:10.1101/gr.105106.110
..., Toronto, Ontario M5T 3H7, Canada ↵ 12 These authors contributed equally to this work. Abstract Mutational screens are an effective means used in the functional annotation of a genome. We present a method for a mutational screen of the mouse X chromosome using gene trap...
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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
...genes In order to understand better the evolution of micro-exon genes, the MEG-3 family was chosen since it contained multiple closely related members, well described in the assembled sequence. Figure 2 illustrates the structure of the four members of this family that form a gene cluster on a chromosome...
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LETTER: A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells
- Guglielmo Roma,
- Gilda Cobellis,
- Pamela Claudiani,
- Francesco Maione,
- Pedro Cruz,
- Gaetano Tripoli,
- Marco Sardiello,
- Ivana Peluso,
- and Elia Stupka
Genome Res. July 2007 17: 1051-1060; Published in Advance May 31, 2007, doi:10.1101/gr.5720807
...performed the first genome-wide analysis of the mouse ES cell transcriptome using ∼250,000 gene trap sequence tags deposited in public databases. We unveiled &gt;8000 novel transcripts, mostly non-coding, and &gt;1000 novel alternative and often tissue-specific exons of known genes. Experimental...
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METHODS: Genomewide Trapping of Genes that Encode Secreted and Transmembrane Proteins Repressed by Oncogenic Signaling
- Mathias Gebauer,
- Harald von Melchner,
- and Thomas Beckers
Genome Res. November 1, 2001 11: 1871-1877; doi:10.1101/gr.202601
...antigen. Molecular analysis of a random sample of NeoR clones revealed that the U3Ceo gene trap preferentially disrupted genes coding for secreted and transmembrane proteins. In each case, the signal sequence of the endogenous gene was fused in-frame to the CD2/neomycin–phosphotransferase reporter gene...

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