Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome

Abstract

We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed draft of the mouse genome. Using this mapping, we identified 3674 mouse genes with multiple transcripts, of which 1098 have splice variants. All but 532 of 21,076 clones (97.5%) mapped to the genome assembly. Alignments of cDNA clone sequences with proteins show that much of the detected splice variation alters coding regions and affects the translated protein. We developed novel analytical techniques to classify observed splice variation and to assess the relation between splice variation and alternative transcription. This analysis indicates that an alternative choice of transcription start or polyadenylation signal frequently induces splice variation.High-quality, full-length cDNA sequences mapped to a highquality complete genome assembly are crucial for the comprehensive analysis of splice variation. Analysis of 21,076 fulllength mouse cDNA clone sequences (RIKEN Genome Exploration Group Phase II Team and FANTOM Consortium. 2001) and of mouse RefSeq sequences (Pruitt and Maglott 2001) mapped to the complete mouse genome assembly (ftp:// ftp.ensembl.org/pub/assembly/mouse/mgsc_assembly_3) reveals numerous and complex patterns of splice variation. We developed stringent computational filters to identify and classify splice variants while eliminating cloning, sequencing, and mapping errors. Our computational pipeline identified 3674 mouse genes with multiple transcripts, 1098 of which (30%) have splice variants (Fig. 1). A total of 971 (88%) of the genes with alternative transcripts closely matched GenBank proteins (Benson et al. 2000). The protein-to-DNA alignments indicate that most of the splice variation affects transcriptcoding regions. The type of variation observed in initial and terminal exons indicates that alternative use of transcription start site and polyadenylation signals may be frequently responsible for the choice of splice signals flanking these exons.The variant transcripts reveal many known and novel forms of proteins, including variants of the myosin light chain, phospholipase A2, and a potassium ion channel with alternative 5Ј protein sequences, as well as a uridine diphosphate (UDP)-galactose transporter-related protein, variants of osmosis-responsive factor with different 5Ј untranslated region (UTR) sequences, and a new form of seryl-tRNA synthase with an internal in-frame extra coding exon. These examples illustrate the breadth of protein function affected by splice variation. They also illustrate a class of variation well represented in our data set, alternative exons possibly associated with alternative start of transcription.Prior large-scale studies of splice variation have used expressed sequence tag (EST) data to focus on two important (2000) used an alternative approach for identifying novel gene forms; they compiled a dataset of well-curated spliceosomal introns and identified alternat...

Two Distinct Forms ofM-Locus Protein Kinase Localize to the Plasma Membrane and Interact Directly withS-Locus Receptor Kinase to Transduce Self-Incompatibility Signaling inBrassica rapa

“…The resulting MLPKf2 isoform encodes a protein sequence identical to the MLPKf1 isoform, excepting the N terminus. Such expression systems, called alternative first exons (AFEs), in which the first exon of one splice variant of a gene is located within an intronic region of another variant, have been well documented in mammals and are suggested to contribute to the diversification of gene expression Zavolan et al, 2002). Although some AFEs merely change the 59-untranslated region and lead to no protein differences, many AFEs alter the N termini of the translated proteins, as is the case with MLPK.…”

In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons

“…Several genome-wide comparisons of expressed sequence tags or full-length cDNA clones with the genomic draft of human and mouse have been carried out to investigate the extent of alternative splicing in the respective genome. 43,44 It suggests itself to use these databases for a genomic comparison of alternatively spliced genes of human and mouse. 7,45 Such detailed comparisons will shed more light on the difference between the alternative splice forms and elucidate to what extent our finding can be generalized or if it is specific for the NF1 and the other investigated genes.…”

Detection and evaluation of intron retention events in the human transcriptome

“…It seems that at least half of all human genes undergo alternative splicing, but the right number probably will exceed that because the detection of splicing variants of lowly expressed genes is difficult (Kan et al 2002;Zavolan et al 2002). The biological significance of alternative splicing is well documented for several models.…”