ArticleNucleic acids research2003
Detection and analysis of spliced chimeric mRNAs in sequence databanks.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- A non-mutatedFrontiers in oncology · 2023Article
- Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells.NAR genomics and bioinformatics · 2021Article
- ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.Nucleic acids research · 2020Article
- Pharmacogenetic and pharmacogenomic discovery strategies.Cancer drug resistance (Alhambra, Calif.) · 2019Review
- Cancer transcriptome profiling at the juncture of clinical translation.Nature reviews. Genetics · 2018Review
- Identification ofOncotarget · 2017Article
- ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.Nucleic acids research · 2017Article
- mRNA trans-splicing in gene therapy for genetic diseases.Wiley interdisciplinary reviews. RNA · 2016Review
- Evolutionary Insights into RNA trans-Splicing in Vertebrates.Genome biology and evolution · 2016Review
- Article
- Repair of rhodopsin mRNA by spliceosome-mediated RNA trans-splicing: a new approach for autosomal dominant retinitis pigmentosa.Molecular therapy : the journal of the American Society of Gene Therapy · 2015Article
- ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.Nucleic acids research · 2015Article
- Article
- Homologous SV40 RNA trans-splicing: a new mechanism for diversification of viral sequences and phenotypes.RNA biology · 2013Article
- ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.Nucleic acids research · 2013Article
- Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.Neoplasia (New York, N.Y.) · 2012Article
- ChimerDB 2.0--a knowledgebase for fusion genes updated.Nucleic acids research · 2010Article
- Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing.Nucleic acids research · 2009Article
- ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs).BMC genomics · 2007Article
- HYBRIDdb: a database of hybrid genes in the human genome.BMC genomics · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
We have developed a databank screening procedure, the In Silico Trans-splicing Retrieval System (ISTReS), to identify heterologous, spliced mRNAs with potential origin from chromosomal translocations, mRNA trans-splicing and multi-locus transcription. A parsing algorithm to screen cDNA versus genome Blast outputs was implemented. Key filtering criteria were Blast scores of > or =300, match lengths of > or =95% of the query sequences, junction of the two partners at exon-exon borders and concordant 'sense/sense' reading orientation. ISTReS was validated by the successful identification of bona fide chromosomal translocation-derived fusion transcripts in the HGI and RefSeq databanks. The performance of ISTReS was verified against recently identified chimeric antisense transcripts, where it revealed essentially no independent proof of antisense transcription and absence of exon-exon borders at the chimeric join, consistent with an artefactual origin. Analysis of the UNIGENE database revealed 21 742 chimeric sequences overall that correspond to approximately 1% of the database transcripts. Novel FOP-Rho GAP and methionyl tRNA synthetase-advillin chimeric mRNAs with the canonical features of heterologous-genes spliced-transcripts were identified among 246 chimeras from the RefSeq databank. This suggests a frequency of canonically-spliced chimeras of approximately 1% of all the hybrid sequences in current databanks. These findings demonstrate the efficiency of ISTReS and the overall feasibility of sequence/structure-based strategies to search for chimeric mRNAs candidate to derive from the splicing of heterologous transcripts.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.