Intrinsic differences between authentic and cryptic 5' splice sites
Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5′ splice sites (5′ss), we systematically analyzed a set of 76 cryptic 5′ss derived from 46 human genes. These cryptic 5′ss have a similar...
| Main Authors: | , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2012
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| Online Access: | https://hdl.handle.net/10356/95535 http://hdl.handle.net/10220/8876 |
| _version_ | 1826122641317036032 |
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| author | Krainer, Adrian R. Sachidanandam, Ravi Roca, Xavier |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Krainer, Adrian R. Sachidanandam, Ravi Roca, Xavier |
| author_sort | Krainer, Adrian R. |
| collection | NTU |
| description | Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5′ splice sites (5′ss), we systematically analyzed a set of 76 cryptic 5′ss derived from 46 human genes. These cryptic 5′ss have a similar frequency distribution in exons and introns, and are usually located close to the authentic 5′ss. Statistical analysis of the strengths of the 5′ss using the Shapiro and Senapathy matrix revealed that authentic 5′ss have significantly higher score values than cryptic 5′ss, which in turn have higher values than the mutant ones. β‐Globin provides an interesting exception to this rule, so we chose it for detailed experimental analysis in vitro. We found that the sequences of the β‐globin authentic and cryptic 5′ss, but not their surrounding context, determine the correct 5′ss choice, although their respective scores do not reflect this functional difference. Our analysis provides a statistical basis to explain the competitive advantage of authentic over cryptic 5′ss in most cases, and should facilitate the development of tools to reliably predict the effect of disease‐associated 5′ss‐disrupting mutations at the mRNA level. |
| first_indexed | 2024-10-01T05:51:29Z |
| format | Journal Article |
| id | ntu-10356/95535 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:51:29Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | ntu-10356/955352023-02-28T17:03:43Z Intrinsic differences between authentic and cryptic 5' splice sites Krainer, Adrian R. Sachidanandam, Ravi Roca, Xavier School of Biological Sciences DRNTU::Science::Biological sciences Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5′ splice sites (5′ss), we systematically analyzed a set of 76 cryptic 5′ss derived from 46 human genes. These cryptic 5′ss have a similar frequency distribution in exons and introns, and are usually located close to the authentic 5′ss. Statistical analysis of the strengths of the 5′ss using the Shapiro and Senapathy matrix revealed that authentic 5′ss have significantly higher score values than cryptic 5′ss, which in turn have higher values than the mutant ones. β‐Globin provides an interesting exception to this rule, so we chose it for detailed experimental analysis in vitro. We found that the sequences of the β‐globin authentic and cryptic 5′ss, but not their surrounding context, determine the correct 5′ss choice, although their respective scores do not reflect this functional difference. Our analysis provides a statistical basis to explain the competitive advantage of authentic over cryptic 5′ss in most cases, and should facilitate the development of tools to reliably predict the effect of disease‐associated 5′ss‐disrupting mutations at the mRNA level. Accepted version 2012-12-21T01:49:51Z 2019-12-06T19:16:45Z 2012-12-21T01:49:51Z 2019-12-06T19:16:45Z 2003 2003 Journal Article Roca, X., Sachidanandam R., & Krainer A. R. (2003). Intrinsic differences between authentic and cryptic 5' splice sites. Nucleic Acids Research, 31(21), 6321-6333. 1362-4962 https://hdl.handle.net/10356/95535 http://hdl.handle.net/10220/8876 10.1093/nar/gkg830 14576320 en Nucleic acids research © 2003 Oxford University Press. This is the author created version of a work that has been peer reviewed and accepted for publication by Nucleic Acids Research, Oxford University Press. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [DOI: http://dx.doi.org/10.1093/nar/gkg830]. application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences Krainer, Adrian R. Sachidanandam, Ravi Roca, Xavier Intrinsic differences between authentic and cryptic 5' splice sites |
| title | Intrinsic differences between authentic and cryptic 5' splice sites |
| title_full | Intrinsic differences between authentic and cryptic 5' splice sites |
| title_fullStr | Intrinsic differences between authentic and cryptic 5' splice sites |
| title_full_unstemmed | Intrinsic differences between authentic and cryptic 5' splice sites |
| title_short | Intrinsic differences between authentic and cryptic 5' splice sites |
| title_sort | intrinsic differences between authentic and cryptic 5 splice sites |
| topic | DRNTU::Science::Biological sciences |
| url | https://hdl.handle.net/10356/95535 http://hdl.handle.net/10220/8876 |
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