Database and analyses of known alternatively spliced genes in plants

Zhou, Yan; Zhou, Chunlong; Ye, Lin; Dong, Jianhai; Xu, Huayong; Cai, Lin; Zhang, Liang; Wei, Liping

doi:10.1016/s0888-7543(03)00204-0

Cited by 41 publications

(23 citation statements)

References 47 publications

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“…Other studies have analyzed even smaller number of genes and transcripts (Kan et al 2002;Gupta et al 2004;Hui et al 2004). The ATS types described thus far include exon skipping, alternative donor site, alternative acceptor site, intron retention, mutually exclusive exons, multiple exon skipping, alternative first exon, alternative last exon, alternative termination in intron, and alternative polyadenylation (Mironov et al 1999;Beaudoing and Gautheret 2001;Modrek et al 2001;Kan et al 2002;Kondrashov and Koonin 2003;Landry et al 2003;Nurtdinov et al 2003;Zhou et al 2003;Galante et al 2004;Zheng 2004). Recent development of a binary code system for exon-intron structures has identified several new patterns of ATS, although these patterns have not been shown (Nagasaki et al 2003).…”

Section: Classification Of Alternative Transcription/splicing (Ats)mentioning

confidence: 99%

Genome-wide assembly and analysis of alternative transcripts in mouse

Sharov

Dudekula

2005

Genome Res.

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To build a mouse gene index with the most comprehensive coverage of alternative transcription/splicing (ATS), we developed an algorithm and a fully automated computational pipeline for transcript assembly from expressed sequences aligned to the genome. We identified 191,946 genomic loci, which included 27,497 protein-coding genes and 11,906 additional gene candidates (e.g., nonprotein-coding, but multiexon). Comparison of the resulting gene index with TIGR, UniGene, DoTS, and ESTGenes databases revealed that it had a greater number of transcripts, a greater average number of exons and introns with proper splicing sites per gene, and longer ORFs. The 27,497 protein-coding genes had 77,138 transcripts, i.e., 2.8 transcripts per gene on average. Close examination of transcripts led to a combinatorial table of 23 types of ATS units, only nine of which were previously described, i.e., 14 types of alternative splicing, seven types of alternative starts, and two types of alternative termination. The 47%, 18%, and 14% of 20,323 multiexon protein-coding genes with proper splice sites had alternative splicings, alternative starts, and alternative terminations, respectively. The gene index with the comprehensive ATS will provide a useful platform for analyzing the nature and mechanism of ATS, as well as for designing the accurate exon-based DNA microarrays.

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Section: Classification Of Alternative Transcription/splicing (Ats)mentioning

confidence: 99%

Genome-wide assembly and analysis of alternative transcripts in mouse

Sharov

Dudekula

2005

Genome Res.

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“…Figure 1 and Figure S1 give some examples of AS patterns observed in the manually curated RefSeq annotation [12]. Despite the ever growing availability of gene annotations the lack of a universal reference definition of AS and hence of the corresponding categories of AS events prevent AS databases (e.g., AEdb [13], ASD [14], ATD [15], Hollywood [16], PASDB [17], SpliceNest [18], PALS db [19], SpliceDB [20], AsMamDB [21], HASDB [22], ProSplicer [23], EuSplice [24], ASAPII [25] etc. …), from the automatic identification and update of the AS landscape that characterizes the transcriptome from a particular cell type or condition.…”

Section: Introductionmentioning

confidence: 99%

A General Definition and Nomenclature for Alternative Splicing Events

Sammeth¹,

Foissac²,

Guigó³

2008

SciVee

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Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific ''AS code'' to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part-in human more than a quarter-of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS.

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“…A few AS events were identified experimentally in plants, including genes involved in splicing (23, 24), transcription (25), flowering regulation (26), disease resistance (27), enzyme activities (28,29), and many other physiological processes and functions (19). A database (PASDB) collecting known alternatively spliced genes in plants is available at http:͞͞pasdb.genomics.org.cn (30). Although the prevalence of AS is not yet clear in plants, it is now recognized as playing an important role in the generation of plant proteome diversity (31).…”

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confidence: 99%

Genomewide comparative analysis of alternative splicing in plants

Wang

Brendel

2006

Proc. Natl. Acad. Sci. U.S.A.

486

480

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Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here exon skipping ͉ intron retention ͉ non-sense-mediated decay ͉ spliced alignment ͉ conserved alternative splicing A lternative splicing (AS) is an important posttranscriptional regulatory mechanism that can increase protein diversity and affect mRNA stability (1, 2). Relative to the predominant transcript isoform, different types of AS have been observed, including exon skipping (ExonS), alternative donor (AltD) or acceptor (AltA) site, and intron retention (IntronR) ( Fig. 1; reviewed in ref.3). AS has been extensively studied by EST͞ cDNA-based analysis in mammalian systems, and 35-60% human genes were suggested to be alternatively spliced (4-9). In humans, ExonS is the most common type (58% of the total number of AS events are ExonS events involving a single exon, and 11% are ExonS events in which multiple exons are skipped in tandem) (4). IntronR is the least common type of AS in humans (5%) (4); Ϸ70-88% of the AS events occur in protein coding regions (reviewed in ref. 10), and approximately onethird produce premature termination codons (PTCs) (11). These PTC-containing transcripts are apparent targets for non sensemediated mRNA decay (NMD) (11). Not all of the predicted AS are real and functional, because many possible sources of false positives exist (10). An AS event has been defined as functional ''if it is required during the life cycle of the organism and activated in a regulated manner'' (12). To identify functional AS events, conserved AS events between human and mouse were studied (12-17), with the assumption that conservation indicates function. Twenty-five percent of a set of 980 ExonS events in human were found to be conserved in mouse (12). Another study reported that Ϸ10% of human gene loci with mouse orthologs show conserved AS events (15).The splicing mechanism in plants is generally conserved compared with mammals (18, 19). However, introns in plant are usually short in length and U-rich (18-20), with a much less apparent polypyrimidine tract near the 3Ј splice site than in mammals (21). Our recent genomewide survey on Arabidopsis splicing-related genes revealed variations in SR proteins and hnRNP proteins between plants and mammals, suggesting plantspecific differences in splicing-regulation mechanisms (22). A few AS events were identified experimentally in plants, including genes involved in splicing (23, 24), transcription (25), flowering regulation (26), disease resistance (27), enzyme activities (28, 29), and many other physiological processes and functions (19). A database (PASDB) collecting known alternatively spliced genes in plants is available at http:͞͞pasdb.genomics.org.cn (30).

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Database and analyses of known alternatively spliced genes in plants

Cited by 41 publications

References 47 publications

Genome-wide assembly and analysis of alternative transcripts in mouse

Genome-wide assembly and analysis of alternative transcripts in mouse

A General Definition and Nomenclature for Alternative Splicing Events

Genomewide comparative analysis of alternative splicing in plants

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