Abstract:
:Alternatively spliced introns are the ones that are usually spliced but can be occasionally retained in a transcript isoform. They are the most frequently used alternative splice form in plants (~50% of alternative splicing events). Chlamydomonas reinhardtii, a unicellular alga, is a good model to understand alternative splicing (AS) in plants from an evolutionary perspective as it diverged from land plants a billion years ago. Using over 7 million cDNA sequences from both pyrosequencing and Sanger sequencing, we found that a much higher percentage of genes (~20% of multi-exon genes) undergo AS than previously reported (3-5%). We found a full component of SR and SR-like proteins possibly involved in AS. The most prevalent type of AS event (40%) was retention of introns, most of which were supported by multiple cDNA evidence (72%) while only 20% of them have coding capacity. By comparing retained and constitutive introns, we identified sequence features potentially responsible for the retention of introns, in the framework of an "intron definition" model for splicing. We find that retained introns tend to have a weaker 5' splice site, more Gs in their poly-pyrimidine tract and a lesser conservation of nucleotide 'C' at position -3 of the 3' splice site. In addition, the sequence motifs found in the potential branch-point region differed between retained and constitutive introns. Furthermore, the enrichment of G-triplets and C-triplets among the first and last 50 nt of the introns significantly differ between constitutive and retained introns. These could serve as intronic splicing enhancers. All the alternative splice forms can be accessed at http://bioinfolab.miamioh.edu/cgi-bin/PASA_r20140417/cgi-bin/status_report.cgi?db=Chre_AS .
journal_name
Plant Mol Bioljournal_title
Plant molecular biologyauthors
Raj-Kumar PK,Vallon O,Liang Cdoi
10.1007/s11103-017-0605-9subject
Has Abstractpub_date
2017-06-01 00:00:00pages
253-265issue
3eissn
0167-4412issn
1573-5028pii
10.1007/s11103-017-0605-9journal_volume
94pub_type
杂志文章abstract::The gene for the membrane polypeptide D2 has been mapped on the pea (Pisum sativum) chloroplast genome. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of MW 39.5 kD. A potential ribosome binding site is located 6 nucleoti...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00029654
更新日期:1984-07-01 00:00:00
abstract::The Arabidopsis ga1 mutant has very low levels of endogenous, active gibberellins and thus has an extreme dwarf phenotype; application of GA3 induces stem elongation and flower development. To test the hypothesis that GA action in this system involves changes in gene expression, we have cloned mRNAs whose abundance ch...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00023557
更新日期:1994-02-01 00:00:00
abstract::The chloroplast gene for the epsilon subunit (atpE) of the CF1/CF0 ATPase in the green alga Chlamydomonas reinhardtii has been localized and sequenced. In contrast to higher plants, the atpE gene does not lie at the 3' end of the beta subunit (atpB) gene in the chloroplast genome of C. reinhardtii, but is located at a...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00025326
更新日期:1987-03-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:2003-03-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00037068
更新日期:1991-10-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00042073
更新日期:1995-08-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/B:PLAN.0000028775.58537.fe
更新日期:2004-01-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1006030007333
更新日期:1998-08-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00027365
更新日期:1993-08-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-010-9615-6
更新日期:2010-06-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00019182
更新日期:1995-01-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1006338401808
更新日期:1999-11-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00028892
更新日期:1992-12-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-006-0054-3
更新日期:2006-08-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-005-2564-9
更新日期:2006-01-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00040726
更新日期:1996-08-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-009-9585-8
更新日期:2010-03-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-005-8519-3
更新日期:2005-09-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:2014-07-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1992-10-01 00:00:00
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pub_type: 杂志文章
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更新日期:1991-03-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1994-10-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:2008-07-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1998-11-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1994-01-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1993-09-01 00:00:00
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更新日期:2007-07-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:2010-09-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
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更新日期:1994-10-01 00:00:00