Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it>
<p>Abstract</p> <p>Background</p> <p>Around 14% of protein-coding genes of <it>Arabidopsis thaliana </it>genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-06-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/10/102 |
| _version_ | 1818927269374066688 |
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| author | Loraine Ann E Patel Ketan S English Adam C |
| author_facet | Loraine Ann E Patel Ketan S English Adam C |
| author_sort | Loraine Ann E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Around 14% of protein-coding genes of <it>Arabidopsis thaliana </it>genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in <it>Arabidopsis</it>, the relative expression level of individual splicing variants is unknown.</p> <p>Results</p> <p>We investigated prevalence of alternative splicing (AS) events in <it>Arabidopsis thaliana </it>using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.</p> <p>Conclusions</p> <p>Currently available evidence from ESTs indicates that alternative splicing in <it>Arabidopsis </it>occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of <it>Arabidopsis </it>genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.</p> |
| first_indexed | 2024-12-20T03:10:20Z |
| format | Article |
| id | doaj.art-d53cc5f1e43c454ba4a0679efc60fb4c |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-20T03:10:20Z |
| publishDate | 2010-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-d53cc5f1e43c454ba4a0679efc60fb4c2022-12-21T19:55:29ZengBMCBMC Plant Biology1471-22292010-06-0110110210.1186/1471-2229-10-102Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it>Loraine Ann EPatel Ketan SEnglish Adam C<p>Abstract</p> <p>Background</p> <p>Around 14% of protein-coding genes of <it>Arabidopsis thaliana </it>genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in <it>Arabidopsis</it>, the relative expression level of individual splicing variants is unknown.</p> <p>Results</p> <p>We investigated prevalence of alternative splicing (AS) events in <it>Arabidopsis thaliana </it>using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.</p> <p>Conclusions</p> <p>Currently available evidence from ESTs indicates that alternative splicing in <it>Arabidopsis </it>occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of <it>Arabidopsis </it>genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.</p>http://www.biomedcentral.com/1471-2229/10/102 |
| spellingShingle | Loraine Ann E Patel Ketan S English Adam C Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> BMC Plant Biology |
| title | Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> |
| title_full | Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> |
| title_fullStr | Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> |
| title_full_unstemmed | Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> |
| title_short | Prevalence of alternative splicing choices in <it>Arabidopsis thaliana</it> |
| title_sort | prevalence of alternative splicing choices in it arabidopsis thaliana it |
| url | http://www.biomedcentral.com/1471-2229/10/102 |
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