Human Molecular Genetics, 2001, Vol. 10, No. 23 2661-2669
© 2001 Oxford University Press
Origin of alternative splicing by tandem exon duplication
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
Received July 9, 2001; Revised and Accepted September 10, 2001.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For
10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes. |
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Recent sequencing of complete eukaryotic genomes showed that the number of genes in complex organisms is surprisingly small. Humans appear to have only approximately 1.5 times as many genes as a relatively simple nematode, Caenorhabditis elegans (approximately 30 000 versus approximately 20 000), and approximately three times as many as the most complex bacteria, e.g. Streptomyces (1–4). The fruit fly Drosophila melanogaster, an organism that is undoubtedly more complex than C.elegans, paradoxically has less than 15 000 genes. This lack of correlation between the complexity of an organisms and the number of genes it has may be partially explained if a gene often codes for more than one protein, owing to alternative splicing. Indeed, alternative splicing is widespread in multicellular eukaryotes, with as many as one in every three human genes producing multiple isoforms (5,6), although even this figure is largely accepted to be an underestimate (6–8). Individual genes with mutually alternate, alternative exons theoretically are capable of producing many more protein isoforms than there are genes in the entire genome (reviewed in 8). Therefore, the ability of alternative splicing to create diversity in the proteome may hold the key to at least some of the observed complexity of the eukaryotic organisms.
At the genome level, classification of the modes of alternative splicing, that includes all possible combinations of the intron–exon structure, has been developed (9). However, to address the impact of alternative splicing on the proteome, a protein-level classification is more relevant. Alternative splicing may affect the protein sequence in two ways: (i) by deleting or inserting a sequence and creating long and short isoforms, with the short isoform being a subsequence of the long one, or (ii) by substituting one segment of the amino acid sequence for another, with each isoform having its own, unique subsequence. The first mode of alternative splicing is more common (5,10) and is primarily responsible for generation of specific regulators of protein function, with the shorter form often being a dominant-negative regulator of the longer form’s activity [for example (11–14)]. In contrast, the second mode is capable of creating, from mutually exclusive alternative sequences, the multitude of functionally distinct protein isoforms and, thus, might have a crucial role in the evolution of complex organisms.
Gene duplication is, arguably, the most common mechanism for creating functional novelty at the level of genes (15–17). Therefore, it seems reasonable to hypothesize that some of the mutually exclusive exons involved in substitution-type alternative splicing might also have evolved by intragenic duplication. Following this reasoning and several reports of probable origin of alternative sequences by duplication (18–23), we sought to investigate the role of exon duplication in the evolution of alternative splicing.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Using proteins from the SwissProt database that were annotated as alternatively spliced, we created a non-redundant data set of 575 substitution alternative splicing cases (Materials and Methods). The difficulty in identifying diverged duplicates among alternatively spliced sequences lies in the fact that they are typically short (median length 33 amino acids), which hampers detection of reliable sequence similarity between diverged duplicates with conventional sequence analysis methods. The initial screening for duplicated sequences involved comparing the two alternatively spliced sequences using the BLASTP program (24). In 109 cases, an alignment with a score above the cut-off expected value of 10 was produced, and these cases were further investigated. To search for possible duplications in this set, we exploited the conservation of the protein segments subject to alternative splicing in homologous proteins from other species.
Initially, we attempted to generate hidden Markov models [HMM (25)] from multiple alignments of alternatively spliced protein segments with the corresponding sequences from orthologs and to use these HMMs for detecting duplicates among alternatively spliced sequences. However, this method proved to be insufficiently sensitive (data not shown), so we turned to analysis of conserved amino acid patterns. For each pair of alternative sequences, a pattern of conserved amino acid residues was derived from the BLAST alignment and run against the SwissProt and TrEMBL databases using the ScanProsite program. When the pattern of amino acid identities and similarities that is conserved between the alternative sequences retrieved exclusively homologs of the corresponding protein (as evaluated by examination of the respective BLAST search results), this was considered an indication that the alternative sequences were related through duplication. Conversely, when the pattern was not selective, i.e. retrieved sequences of non-homologous proteins, the duplication hypothesis was rejected. To account for the possibility that the derived pattern was overly specific, in cases when no sequences other than the alternative sequences themselves were detected, the reverse search was performed. A multiple alignment of one of the alternative sequences with the corresponding sequences from homologous proteins was constructed, and the pattern of conserved residues was extracted and run against the SwissProt and TrEMBL databases using the ScanProsite program. When the second alternative sequence was detected with this pattern without any false positives retrieved, this was accepted as support for the duplication hypothesis.
Of the 575 alternative splicing events in our initial set, this approach produced evidence of origin by duplication for 50 (9%) (Table 1). The alternative sequences, for which evidence of duplication was obtained by amino acid pattern analysis, were at least 30% similar (Fig. 1). Given the characteristic length of alternative sequences, duplicated sequences with greater divergence probably retained too little information to be detected by these methods. No duplicated alternative sequences with >90% similar residues were detected. This might indicate that such intragenic duplications undergo accelerated evolution immediately after duplication. Alternatively, or additionally, this might be owing to the difficulty of recognizing alternative isoforms when they are nearly identical, especially when the identification involved cDNA screening. Thus, the number of detected cases of duplication among alternative sequences appears to be a conservative estimate.
|
|
The observed conservation of amino acid patterns between duplicated alternative sequences and their counterparts in homologous proteins from distantly related species implies structural and functional conservation. This is supported by the observation that the pattern of variability in non-conserved positions of duplicated alternative sequences typically mimics that in homologs from other species; changes that are not already ‘pre-approved’ by selection during evolution are uncharacteristic (Fig. 2). Thus, whatever functional variation is achieved by alternating duplicated sequences, it seems to be mediated by subtle changes in the structures of the proteins involved.
|
For cases of internal alternative splicing in which the gene structure was available in the literature or could be determined by the BLAT server (Materials and Methods), the unit of duplication was always one exon and the duplication involved consecutive exons (tandem duplication). In the case of N- and C-terminal alternative splicing, several exceptions were found, where duplication encompassed more than one exon, such as in the Drosophila passover protein (21). Furthermore, several cases were identified where more than one duplication event apparently has been involved in the evolution of the alternatively spliced sequences. For example, in the Drosophila troponin, four exons seem to share a common ancestor (26). No cases of partial exon duplication were detected.
The presence of homologous alternative splicing events in homologous genes in different species makes it possible to conclude that emergence of alternative splicing in the given gene antedates the last common ancestor (LCA) of the two lineages. Of the 50 cases of alternative splicing that seem to have evolved by duplication, 15 had homologs with demonstrated alternative splicing in related species (Table 1). We also utilized a less direct approach for dating the duplication events, namely search for orthologous sequences that were significantly more similar to one alternative exon than to the other (Materials and Methods). The rationale behind this approach lies in the possibilities that alternative splicing remains undiscovered or that duplicated exons were secondarily lost in some lineages. As an example of this approach, one of the duplicated exons in a human gene is significantly more similar to a homologous exon in a Xenopus laevis gene, and the other exon is more similar to a Cyprinus carpio homolog (Fig. 2A). If we assume that the Cyprinus homolog resembles the ancestral state, it can be inferred that the duplication of the exon occurred, at the latest, in the LCA of the human and frog lineages.
We applied this approach to the 50 duplicated alternative splicing cases, to estimate the approximate time of exon duplication. Of the 15 cases which were supported by data on alternative splicing in orthologs from different species, this dating approach implied a more distant time of emergence for only three cases, whereas, for the other 12 cases, the estimate was either more conservative or identical to that suggested by homologous alternative splicing. A combination of these results and the data on homologous alternative splicing is shown in Table 1 as our estimate of the LCA in which the duplication could have occurred. Of the 29 dated cases, the most common time frame for the emergence of the duplication was in the LCA of the mammalian orders, of which there were 14 cases. In two instances, the duplication was mapped to the LCA of mouse and rat. In 13 remaining cases, the duplication appeared to be more ancient, with five cases antedating the LCA of mammals and chicken, three the LCA of mammals and frog, two the LCA of mammals and bony fish, and two the LCA of mammals and nematodes (Table 1). Although, because of the short length of the duplicated exons, statistical artifacts cannot be ruled out in some of these cases, the results suggest at least some duplications leading to substitution alternative splicing have persisted for hundreds of millions of years.
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
From an evolutionary perspective, exon duplication could be viewed in the same light as gene duplication, which is usually considered to be the principal path of functional diversification of proteins and emergence of new functions. The original hypothesis on the role of gene duplication in evolution, proposed in 1970 by Susumu Ohno, holds that one copy of a duplicated gene becomes functionally redundant and, accordingly, free of selective constraints, which usually leads to its elimination, but in the rare cases of beneficial mutations, could lead to a new gene function (15–17,27,28). However, such an asymmetry in the evolution of duplicated genes does not seem to be common and, therefore, alternative theoretical frameworks have been proposed to describe evolution of duplicates. One of these postulates ‘subfunctionalization’, i.e. allocation of distinct sub-functions of the original gene to the duplicates, making both duplicates indispensable, as a result of mutations impairing each of the sub-functions in one of the duplicates (29,30). Another hypothesis postulates that a pair of duplicated genes could specialize and improve in different functions of the ancestral gene as a result of positive selection (31).
All these considerations are also applicable to exon duplications, but the notion of specialization seems to be particularly relevant because, assuming that substitution alternative splicing has a functional role, diversification of the relatively small alternative exons may result in incremental changes in protein function. The theory of evolution of duplicated genes by ‘subfunctionalization’ is based on the assumption that, after a duplication event, the level of expression of the duplicated gene is doubled, thus relaxing the level of selection on degenerate mutations (29,30). However, after exon duplication, the level of expression and, therefore, the strength of selection is likely to remain the same, thus eliminating the possibility or the need for a relaxation of selection against degenerate mutations. Thus, if both duplicated exons are (alternately) translated immediately after the duplication event, both of them will be subject to stabilizing selection from the moment of their emergence. Accordingly, the initial apparent absence of selection after a duplication, which is a prerequisite of both the original Ohno’s model and the ‘subfunctionalization’ model, does not seem to apply to duplicated exons. This appears to favor the specialization model for tandem exon duplications.
That exon duplication is likely to be non-lethal only when alternative splicing is established immediately after such an event, is suggested by examination of the structure of the duplicated exons. For 14 of the 25 sets of internal or N-terminal, alternatively spliced, duplicated exons, the combined length was not a multiple of 3 (Table 1), so that retention of both duplicated exons in the mRNA would result in a frame shift. It is possible that the fact that there are many cases of alternative splicing, in which the sum of the lengths of the alternative exons does not divide by three, does not reflect the ancestral condition due to intron sliding. However, since intron sliding appears to be rare (32–34), the alternative exons are likely to have been mutually exclusive and, therefore, alternatively spliced, from the moment of their emergence.
Although we identified exon duplications for only 9% of the substitution alternative splicing cases in our data set, it is likely that this number is an underestimate, perhaps substantial, of the actual number of cases that have originated via this route. This is primarily because alternative exons are typically short and many could have diverged beyond recognition of sequence similarity. Moreover, tandem exon duplication is, at present, the only mechanism for evolution of substitution alternative splicing that is directly supported by sequence data. The other imaginable mechanisms, which would result in unrelated alternative sequences, include duplication of a different exon from the same gene, duplication of an exon from a different gene, or emergence of an exon from an intron sequence. At present, in the absence of evidence in support of these routes, tandem exon duplication appears to be a major, if not the principal, evolutionary source of substitution alternative splicing.
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Alternative splicing data set
Since the SwissProt database contains a list of genes that have been annotated as alternatively spliced, all analyzed protein sequences were extracted from SwissProt by using ‘alternative splicing’ as a keyword. Because SwissProt does not include information about the gene structure of the alternative forms, and to avoid including potential sequencing and annotation errors, only the cases of substitution alternative splicing in which both the original and the alternative sequence were longer than nine amino acids were retained. To create a non-redundant set of alternatively spliced gene forms, only one of each set of homologous alternatively spliced forms (those that produced a collinear BLAST alignment including the alternative sequence) was retained in the data set. The final data set included 575 instances of substitution alternative splicing. To determine the gene structure of alternatively spliced human genes, the cDNAs were aligned with the rough draft of the human genome (4) using the BLAT server at the University of California-Santa Cruz (http://genome.ucsc.edu/).
Sequence analysis
Protein sequence database searches were performed using the BLASTP program (24) and the non-redundant database at the National Center for Biotechnology Information (NIH, Bethesda). Pairwise sequence comparisons were performed using the BLASTP program with default parameters, but using the BLOSUM80 substitution matrix; for each comparison, one of the analyzed sequences was converted to a ‘blastable’ database by using the FORMATDB program and the other sequence was used as a query to search this database (24). Multiple alignments of protein sequences were constructed using the ClustalX program (35). Amino acid pattern search was performed using the ScanProsite program at the Swiss Institute of Bioinformatics (36).
To identify the LCA, in which the duplication of the exon is likely to have occurred, the significance of the observation that a homologous exon is more similar to one of the alternative exons than to the other was assessed using the Mann–Whitney U test (P < 0.01). For each of the alternative exons, the most distant statistically similar homolog, such that, in the species tree, the corresponding species were closer to each other than to the species with the alternative splicing, was used for this test. The duplication was then dated to the LCA of the lineage with the alternative splicing and lineage, from which the closest of the homologs was derived. The SwissProt entries for all analyzed alternatively spliced gene forms and the alignments of duplicated alternative exons are available at ftp://ncbi.nlm.nih.gov/pub/Koonin/alternative_splicing
|
FOOTNOTES |
|---|
+ To whom correspondence should be addressed. Tel: +1 301 535 5913; Fax: +1 301 435 7794; Email: koonin@ncbi.nlm.nih.gov
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
1 Casjens, S. (1998) The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet., 32, 339–377[Web of Science][Medline]
2 The C.elegans Sequence Consortium (1998) Genome sequence of the nematode C.elegans: a platform for investigating biology. Science, 282, 2012–2018.
3 Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185–2195.
4 International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860–921.[Medline]
5 Mironov, A.A., Fickett, J.W. and Gelfand, M.S. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288–1293.
6 Hanke, J., Brett, D., Zastrow, I., Aydin, A., Delbruck, S., Lehmann, G., Luft, F., Reich, J. and Bork, P. (1999) Alternative splicing of human genes: more the rule than the exception? Trends Genet., 15, 389–390.[Web of Science][Medline]
7 Croft, L., Schandorff, S., Clark, F., Burrage, K., Arctander, P. and Mattick, J.S. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat. Genet., 24, 340–341.[Web of Science][Medline]
8 Graveley, B.R. (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet., 17, 100–107.[Web of Science][Medline]
9 Breitbart, R.E., Andreadis, A. and Nadal-Ginard, B. (1987) Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes. Annu. Rev. Biochem., 56, 467–495[Web of Science][Medline]
10 Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O. and Zhang, M.Q. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol., 19, 739–756.[Web of Science][Medline]
11 Boise, L.H., Gonzalez-Garcia, M., Postema, C.E., Ding, L., Lindsten, T., Turka, L.A., Mao, X., Nunez, G. and Thompson, C.B. (1993) bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell, 74, 597–608.[Web of Science][Medline]
12 Ross, R.J., Esposito, N., Shen, X.Y., Von Laue, S., Chew, S.L., Dobson, P.R., Postel-Vinay, M.C. and Finidori, J. (1997) A short isoform of the human growth hormone receptor functions as a dominant negative inhibitor of the full-length receptor and generates large amounts of binding protein. Mol. Endocrinol., 11, 265–273.
13 Okada, S., Kao, A.W., Ceresa, B.P., Blaikie, P., Margolis, B. and Pessin, J.E. (1997) The 66-kDa Shc isoform is a negative regulator of the epidermal growth factor-stimulated mitogen-activated protein kinase pathway. J. Biol. Chem., 272, 28042–28049.
14 Srinivasula, S.M., Ahmad, M., Guo, Y., Zhan, Y., Lazebnik, Y., Fernandes-Alnemri, T. and Alnemri, E.S. (1999) Identification of an endogenous dominant-negative short isoform of caspase-9 that can regulate apoptosis. Cancer Res., 59, 999–1002.
15 Ohno, S. (1970) Evolution by Gene Duplication. Springer-Verlag, Berlin, Heidelberg, New York.
16 Li, W.H. (1997) Molecular Evolution. Sinauer, Sunderland, MA.
17 Hughes, A.L. (1999) Adaptive Evolution of Genes and Genomes. Oxford University Press, New York, Oxford.
18 Kim, J., Yim, J.J., Wang, S. and Dorsett, D. (1992) Alternate use of divergent forms of an ancient exon in the fructose-1, 6-bisphosphate aldolase gene of Drosophila melanogaster. Mol. Cell. Biol., 12, 773–783.
19 Bark, I.C. (1993) Structure of the chicken gene for SNAP-25 reveals duplicated exon encoding distinct isoforms of the protein. J. Mol. Biol., 233, 67–76.[Web of Science][Medline]
20 Stewart, M.J. and Denell, R. (1993) The Drosophila ribosomal protein S6 gene includes a 3' triplication that arose by unequal crossing-over. Mol. Biol. Evol., 10, 1041–1047.[Abstract]
21 Crompton, D., Todman, M., Wilkin, M., Ji, S. and Davies, J. (1995) Essential and neural transcripts from the Drosophila shaking-B locus are differentially expressed in the embryonic mesoderm and pupal nervous system. Dev. Biol., 170, 142–58.[Web of Science][Medline]
22 Peixoto, A.A., Smith, L.A. and Hall, J.C. (1997) Genomic organization and evolution of alternative exons in a Drosophila calcium channel gene. Genetics, 145, 1003–1013.[Abstract]
23 Hayward, B.E. and Bonthron, D.T. (1998) Structure and alternative splicing of the ketohexokinase gene. Eur. J. Biochem., 257, 85–91.[Web of Science][Medline]
24 Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402.
25 Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755–763.
26 Barbas, J.A., Galceran, J., Torroja, L., Prado, A. and Ferrus, A. (1993) Abnormal muscle development in the heldup3 mutant of Drosophila melanogaster is caused by a splicing defect affecting selected troponin I isoforms. Mol. Cell. Biol., 13, 1433–1439.
27 Wagner, A. (1998) The fate of duplicated genes: loss or new function? Bioessays, 20, 785–788[Web of Science][Medline]
28 Holland, P.W. (1999) Gene duplication: past, present and future. Semin. Cell Dev. Biol., 10, 541–547.[Web of Science][Medline]
29 Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L. and Postlethwait, J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151, 1531–1545.
30 Lynch, M. and Force, A. (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics, 154, 459–473.
31 Hughes, A.L. (1994) The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci., 256, 119–124.[Medline]
32 Rzhetsky, A., Ayala, F.J., Hsu, L.C., Chang, C. and Yoshida, A. (1997) Exon/intron structure of aldehyde dehydrogenase genes supports the ‘introns-late’ theory. Proc. Natl Acad. Sci. USA, 94, 6820–6825.
33 Stoltzfus, A., Logsdon, J.M.,Jr, Palmer, J.D. and Doolittle, W.F. (1997) Intron ‘sliding’ and the diversity of intron positions. Proc. Natl Acad. Sci. USA, 94, 10739–10744.
34 Rogozin, I.B., Lyons-Weiler, J. and Koonin, E.V. (2000) Intron sliding in conserved gene families. Trends Genet., 16, 430–432.[Web of Science][Medline]
35 Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680
36 Appel, R.D., Bairoch, A. and Hochstrasser, D.F. (1994) A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci., 19, 258–60.[Web of Science][Medline]
37 Kockel, L., Vorbruggen, G., Jackle, H., Mlodzik, M. and Bohmann, D. (1997) Requirement for Drosophila 14–3-3 zeta in Raf-dependent photoreceptor development. Genes Dev., 11, 1140–1147.
38 Kwon, Y.T., Kashina, A.S. and Varshavsky, A. (1999) Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway. Mol. Cell. Biol., 19, 182–193.
39 Varanasi, U., Chu, R., Chu, S., Espinosa, R., LeBeau, M.M. and Reddy, J.K. (1994) Isolation of the human peroxisomal acyl-CoA oxidase gene: organization, promoter analysis, and chromosomal localization. Proc. Natl Acad. Sci. USA, 91, 3107–3111.
40 Diebold, R.J., Koch, W.J., Ellinor, P.T., Wang, J.J., Muthuchamy, M., Wieczorek, D.F. and Schwartz, A. (1992) Mutually exclusive exon splicing of the cardiac calcium channel 
1 subunit gene generates developmentally regulated isoforms in the rat heart. Proc. Natl Acad. Sci. USA, 89, 1497–1501.
41 Kollmar, R., Fak, J., Montgomery, L.G. and Hudspeth, A.J. (1997) Hair cell-specific splicing of mRNA for the 1D subunit of voltage-gated Ca2+ channels in the chicken’s cochlea. Proc. Natl Acad. Sci. USA, 94, 14889–14893.
42 Borsani, G., DeGrandi, A., Ballabio, A., Bulfone, A., Bernard, L., Banfi, S., Gattuso, C., Mariani, M., Dixon, M., Donnai, D. et al. (1999) EYA4, a novel vertebrate gene related to Drosophila eyes absent. Hum. Mol. Genet., 8, 11–23.
43 van der Flier, A., Kuikman, I., Baudoin, C., van der Neut, R. and Sonnenberg, A. (1995) A novel ß 1 integrin isoform produced by alternative splicing: unique expression in cardiac and skeletal muscle. FEBS Lett., 369, 340–344.[Web of Science][Medline]
44 Gross, R.E., Bagchi, S., Lu, X. and Rubin, C.S. (1990) Cloning, characterization, and expression of the gene for the catalytic subunit of cAMP-dependent protein kinase in Caenorhabditis elegans. Identification of highly conserved and unique isoforms generated by alternative splicing. J. Biol. Chem., 265, 6896–6907.
45 Wirz, T., Brandle, U., Soldati, T., Hossle, J.P. and Perriard, J.C. (1990) A unique chicken B-creatine kinase gene gives rise to two B-creatine kinase isoproteins with distinct N termini by alternative splicing. J. Biol. Chem., 265, 11656–11666.
46 Gough, N.R., Hatem, C.L. and Fambrough, D.M. (1995) The family of LAMP-2 proteins arises by alternative splicing from a single gene: characterization of the avian LAMP-2 gene and identification of mammalian homologs of LAMP-2b and LAMP-2c. DNA Cell Biol., 14, 863–867.[Web of Science][Medline]
47 Yu, Y.T., Breitbart, R.E., Smoot, L.B., Lee, Y., Mahdavi, V. and Nadal-Ginard, B. (1992) Human myocyte-specific enhancer factor 2 comprises a group of tissue-restricted MADS box transcription factors. Genes Dev., 6, 1783–1798.
48 Dolce, V., Iacobazzi, V., Palmieri, F. and Walker, J.E. (1994) The sequences of human and bovine genes of the phosphate carrier from mitochondria contain evidence of alternatively spliced forms. J. Biol. Chem., 269, 10451–10460.
49 Kofuji, P., Lederer, W.J. and Schulze, D.H. (1994) Mutually exclusive and cassette exons underlie alternatively spliced isoforms of the Na/Ca exchanger. J. Biol. Chem., 269, 5145–5149.
50 Igarashi, P., Vanden Heuvel, G.B., Payne, J.A. and Forbush, B.,III (1995) Cloning, embryonic expression, and alternative splicing of a murine kidney-specific Na-K-Cl cotransporter. Am. J. Physiol., 269, F405–F418.
51 Helaakoski, T., Veijola, J., Vuori, K., Rehn, M., Chow, L.T., Taillon-Miller, P., Kivirikko, K.I. and Pihlajaniemi, T. (1994) Structure and expression of the human gene for the subunit of prolyl 4-hydroxylase. The two alternatively spliced types of mRNA correspond to two homologous exons the sequences of which are expressed in a variety of tissues. J. Biol. Chem., 269, 27847–27854.
52 Rashbass, J., Taylor, M.V. and Gurdon, J.B. (1992) The DNA-binding protein E12 co-operates with XMyoD in the activation of muscle-specific gene expression in Xenopus embryos. EMBO J., 11, 2981–2990.[Web of Science][Medline]
53 Karlik, C.C., Mahaffey, J.W., Coutu, M.D. and Fyrberg, E.A. (1984) Organization of contractile protein genes within the 88F subdivision of the D.melanogaster third chromosome. Cell, 37, 469–481.[Web of Science][Medline]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  F. Catania, X. Gao, and D. G. Scofield Endogenous Mechanisms for the Origins of Spliceosomal Introns J. Hered., September 1, 2009; 100(5): 591 - 596. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Lin, P. Jiang, S. Shen, S. Sato, B. L. Davidson, and Y. Xing Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes Hum. Mol. Genet., June 15, 2009; 18(12): 2204 - 2214. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Irimia, J. L. Rukov, D. Penny, J. Garcia-Fernandez, J. Vinther, and S. W. Roy Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis Mol. Biol. Evol., February 1, 2008; 25(2): 375 - 382. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Sorek The birth of new exons: Mechanisms and evolutionary consequences RNA, October 1, 2007; 13(10): 1603 - 1608. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Alekseyenko, N. Kim, and C. J. Lee Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes RNA, May 1, 2007; 13(5): 661 - 670. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Zhuo, R. Madden, S. A. Elela, and B. Chabot Modern origin of numerous alternatively spliced human introns from tandem arrays PNAS, January 16, 2007; 104(3): 882 - 886. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. D. Holland, M. T. Fleming, S. Cheek, J. L. Moran, D. R. Beier, and M. H. Meisler De Novo Exon Duplication in a New Allele of Mouse Glra1 (Spasmodic) Genetics, December 1, 2006; 174(4): 2245 - 2247. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. K. Jones, V. Raymond-Delpech, S. H. Thany, M. Gauthier, and D. B. Sattelle The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera Genome Res., November 1, 2006; 16(11): 1422 - 1430. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Gopalapillai, K. Kadono-Okuda, K. Tsuchida, K. Yamamoto, J. Nohata, M. Ajimura, and K. Mita Lipophorin receptor of Bombyx mori: cDNA cloning, genomic structure, alternative splicing, and isolation of a new isoform J. Lipid Res., May 1, 2006; 47(5): 1005 - 1013. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. B. Malko, V. J. Makeev, A. A. Mironov, and M. S. Gelfand Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes Genome Res., April 1, 2006; 16(4): 505 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Shao, V. Shepelev, and A. Fedorov Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans Bioinformatics, March 15, 2006; 22(6): 692 - 698. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. ZHENG, X.-D. FU, and M. GRIBSKOV Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse RNA, December 1, 2005; 11(12): 1777 - 1787. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. P. Cusack and K. H. Wolfe Changes in Alternative Splicing of Human and Mouse Genes Are Accompanied by Faster Evolution of Constitutive Exons Mol. Biol. Evol., November 1, 2005; 22(11): 2198 - 2208. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Xing and C. Lee Colloquium Paper: Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences PNAS, September 20, 2005; 102(38): 13526 - 13531. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Wang, H. Zheng, S. Yang, H. Yu, J. Li, H. Jiang, J. Su, L. Yang, J. Zhang, J. McDermott, et al. Origin and evolution of new exons in rodents Genome Res., September 1, 2005; 15(9): 1258 - 1264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. R. GRAVELEY, A. KAUR, D. GUNNING, S. L. ZIPURSKY, L. ROWEN, and J. C. CLEMENS The organization and evolution of the Dipteran and Hymenopteran Down syndrome cell adhesion molecule (Dscam) genes RNA, October 20, 2004; 10(10): 1499 - 1506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhuang, F. Ma, J. Li-Ling, X. Xu, and Y. Li Comparative Analysis of Amino Acid Usage and Protein Length Distribution Between Alternatively and Non-alternatively Spliced Genes Across Six Eukaryotic Genomes Mol. Biol. Evol., December 1, 2003; 20(12): 1978 - 1985. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Kitamura, Y. Kinoshita, S. Narasaki, N. Nemoto, Y. Husimi, and K. Nishigaki Construction of block-shuffled libraries of DNA for evolutionary protein engineering: Y-ligation-based block shuffling Protein Eng. Des. Sel., October 1, 2002; 15(10): 843 - 853. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Letunic, R. R. Copley, and P. Bork Common exon duplication in animals and its role in alternative splicing Hum. Mol. Genet., June 15, 2002; 11(13): 1561 - 1567. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||