Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Journal of Molecular Evolution

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1007/s00239-008-9187-0PMID 19089307
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Bursicon Gene in Mosquitoes: An Unusual Example of mRNA Trans-splicing

  2007influential reference
• What is a gene, post-ENCODE? History and updated definition.

  2007cited by this paper
• Functional consequences of new exon acquisition in mammalian chromodomain Y-like (CDYL) genes.

  2007cited by this paper
• Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression

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• Tentative Mapping of Transcription-Induced Interchromosomal Interaction using Chimeric EST and mRNA Data

  2007cited by this paper
• Overview: methods and applications for droplet compartmentalization of biology

  2006cited by this paper
• Interchromosomal Trans-Splicing of DMRT1 Gene on Chicken Chromosome Z

  2006influential reference
• Mammalian Transcription in Support of Hybrid mRNA and Protein Synthesis in Testis and Lung*

  2006influential reference
• Alternative trans‐splicing: a novel mode of pre‐mRNA processing

  2006cited by this paper
• CTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1

  2006cited by this paper
• Trans-splicing of the mod(mdg4) Complex Locus Is Conserved Between the Distantly Related Species Drosophila melanogaster and D. virilis

  2005cited by this paper
• Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

  2005cited by this paper
• Origin and evolution of new exons in rodents.

  2005cited by this paper
• Close encounters between active genes in the nucleus

  2005cited by this paper
• Pre-mRNA trans-splicing: from kinetoplastids to mammals, an easy language for life diversity.

  2005influential reference
• Genomic organization of the mouse Msh4 gene producing bicistronic, chimeric and antisense mRNA.

  2004influential reference
• Active genes dynamically colocalize to shared sites of ongoing transcription

  2004cited by this paper
• Alternative splicing and evolution.

  2003cited by this paper
• Alternative trans-splicing of constant and variable exons of a Drosophila axon guidance gene, lola.

  2003influential reference
• A Candidate Chimeric Mammalian mRNA Transcript Is Derived from Distinct Chromosomes and Is Associated with Nonconsensus Splice Junction Motifs

  2003cited by this paper
• Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing.

  2002influential reference
• Alternative pre-mRNA splicing and proteome expansion in metazoans

  2002cited by this paper
• Transcription and nuclear transport of CAG/CTG trinucleotide repeats in yeast.

  2002cited by this paper
• BLAT--the BLAST-like alignment tool.

  2002cited by this paper
• Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila.

  2002influential reference
• Intergenic mRNA Molecules Resulting fromtrans-Splicing*

  2002cited by this paper
• Promoter Choice Determines Splice Site Selection in Protocadherin α and γ Pre-mRNA Splicing

  2002cited by this paper
• Novel Frameshift Mutations near Short Simple Repeats*

  2001cited by this paper
• The sequence of the human genome (abstract only)

  2001cited by this paper
• Evolutionary origin of SL-addition trans-splicing: still an enigma.

  2001cited by this paper
• Alternative splicing: increasing diversity in the proteomic world.

  2001cited by this paper
• Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila

  2001cited by this paper
• The human CYP2C locus: a prototype for intergenic and exon repetition splicing events.

  2000cited by this paper
• Heterogeneous Sp1 mRNAs in Human HepG2 Cells Include a Product of Homotypic trans-Splicing*

  2000cited by this paper
• RNA maturation of the rice SPK gene may involve trans-splicing.

  1999influential reference
• Human Acyl-CoA:Cholesterol Acyltransferase-1 (ACAT-1) Gene Organization and Evidence That the 4.3-Kilobase ACAT-1 mRNA Is Produced from Two Different Chromosomes*

  1999cited by this paper
• Exon repetition in mRNA.

  1999cited by this paper
• RNA molecules containing exons originating from different members of the cytochrome P450 2C gene subfamily (CYP2C) in human epidermis and liver

  1999cited by this paper
• Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei.

  1998cited by this paper
• Frameshift mutants of beta amyloid precursor protein and ubiquitin-B in Alzheimer's and Down patients.

  1998cited by this paper
• Natural trans-splicing in carnitine octanoyltransferase pre-mRNAs in rat liver.

  1998cited by this paper
• A truncated isoform of Ca2+/calmodulin‐dependent protein kinase II expressed in human islets of Langerhans may result from trans‐splicing

  1997cited by this paper
• A potential splicing factor is encoded by the opposite strand of the trans-spliced c-myb exon.

  1992cited by this paper
• Trans-splicing as a possible molecular mechanism for the multiple isotype expression of the immunoglobulin gene

  1991cited by this paper
• Alternative processing of androgen-binding protein RNA transcripts in fetal rat liver. Identification of a transcript formed by trans splicing.

  1991cited by this paper
• The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces.

  1991cited by this paper
• Complex structure and regulation of the ABP/SHBG gene.

  1991cited by this paper
• Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli.

  1990cited by this paper
• Site-directed mutagenesis by overlap extension using the polymerase chain reaction.

  1989cited by this paper
• Immunoglobulin double-isotype expression by trans-mRNA in a human immunoglobulin transgenic mouse.

  1989cited by this paper
• Structural and transcription analysis of two homologous genes for the P700 chlorophyll a‐apoproteins in Chlamydomonas reinhardii: evidence for in vivo trans‐splicing

  1987cited by this paper
• Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts.

  1987cited by this paper
• Sequence the Human Genome

  1986cited by this paper
• Trans splicing of mRNA precursors in vitro.

  1985cited by this paper
• Trans splicing of mRNA precursors.

  1985cited by this paper
• Why genes in pieces?

  1978cited by this paper

• Crosstalk Between R-Loops, RNA/DNA Modifications, and Cell Death Dynamics in Canine Models of Retinitis Pigmentosa

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• Chimerism: A whole new perspective in gene regulation.

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• Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea

  2025cites this paper
• Conserved features and diversity attributes of chimeric RNAs across accessions in four plants

  2024cites this paper
• Identification of circular RNAs hosted by the RPGR ORF15 genomic locus

  2023cites this paper
• Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer

  2022cites this paper
• SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA

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• Discovery and Characterization of Circular and Chimeric RNAs in Complex Diseases

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• Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts

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• Long-read transcriptome sequencing analysis with IsoTools

  2021cites this paper
• The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer.

  2020cites this paper
• Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins.

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• A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens

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• Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras.

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• Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy.

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• Interior circular RNA

  2020cites this paper
• An interstitial peptide is readily processed from within seed proteins.

  2019cites this paper
• LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells

  2019cites this paper
• Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer

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• A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes

  2018cites this paper
• Chimeric RNA in Cancer and Stem Cell Differentiation

  2018cites this paper
• It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research

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• Evidence for transcript networks composed of chimeric RNAs in human cells

  2017cites this paper
• Chimeric RNAs in cancer and normal physiology

  2017cites this paper
• Evolutionary Insights into RNA trans-Splicing in Vertebrates

  2016cites this paper
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  2016cites this paper
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• Recurrent chimeric fusion RNAs in non-cancer tissues and cells

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• Origins of New Genes and Evolution of Their Novel Functions

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• The genesis of new proteins and new biosyntheses

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• Exon circularization requires canonical splice signals.

  2015cites this paper
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• chimeric RNA transcripts Chimeras taking shape : Potential functions of proteins encoded by P < P

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• The Role of Canonical and Noncanonical Pre-mRNA Splicing in Plant Stress Responses

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• Novel domain combinations in proteins encoded by chimeric transcripts

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• ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

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• Chimeric RNAs as potential biomarkers for tumor diagnosis.

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• Using Chimaeric Expression Sequence Tag as the Reference to Identify Three-Dimensional Chromosome Contacts

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• Spatial Proximity and Similarity of the Epigenetic State of Genome Domains

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• Reevaluation of the Reliability and Usefulness of the Somatic Homologous Recombination Reporter Lines

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• Dissect: detection and characterization of novel structural alterations in transcribed sequences

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• Looking ultra deep: short identical sequences and transcriptional slippage

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• Prolonged nerve blockade delays the onset of neuropathic pain

  2012cites this paper
• From Genome-wide Probabilistic Functional Networks to a Model for Physical Chromosome Interactions

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  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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• Trans-splicing in Higher Eukaryotes: Implications for Cancer Development?

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• Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.

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• Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae

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• complexity of the rice transcriptome Deep RNA sequencing at single base-pair resolution reveals high Material Supplemental

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• trans Regulation: do mRNAs have a herd mentality?

  2010cites this paper
• A variant of the KLK 4 gene is expressed as a cis sense – antisense chimeric transcript in prostate cancer cells

  2010influential citation
• Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes

  2010cites this paper
• A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells.

  2010influential citation
• Global analysis of trans-splicing in Drosophila

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• Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

  2010influential citation
• A global view of genomic information--moving beyond the gene and the master regulator.

  2010cites this paper
• Implications of chimaeric non-co-linear transcripts

  2009cites this paper
• Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

  2009cites this paper
• Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.

  2009cites this paper