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<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>

  <div ID="mainWLS" align="center"> <BR>
    <BR>
    <h1 align=center>Identification, characterization, and molecular phylogeny 
      of U12-dependent introns in the <em>Arabidopsis thaliana</em> genome</h1>
    <p align=center>Wei Zhu and Volker Brendel (Nucleic Acid Research 31: 4561-4572)</p>
    <p align=justify>&nbsp;</p>
    <p align=justify><strong><font size="2">ABSTRACT</font></strong></p>
    <p align="justify">U12-dependent introns are spliced by the minor U12-type 
      spliceosome and occur in a variety of eukaryotic organisms, including <em>Arabidopsis</em>. 
      In this study, a set of putative U12-dependent introns was compiled from 
      a large collection of cDNA/EST-confirmed introns in the <em>Arabidopsis</em> 
      thaliana genome by means of high-throughput bioinformatic analysis combined 
      with manual scrutiny. A total of 165 U12-type introns were identified based 
      upon stringent criteria. This number of sequences well exceeds the total 
      number of U12-type introns previously reported for plants and allows more 
      thorough statistical analysis of U12-type signals. Of particular note is 
      the discovery that the distance between the branch site adenosine and the 
      acceptor site ranges from 10 nt to 39 nt, significantly longer than the 
      previously postulated limit of 21 bp. Further analysis indicates that, in 
      addition to the spacing constraint, the sequence context of the potential 
  acceptor site may have an important role in 3&apos;-splice site selection. Several 
      alternative splicing events involving U12-type introns were also captured 
      in this study, providing evidence that U12-dependent acceptor sites can 
      also be recognized by the U2-type spliceosome. Furthermore, phylogenetic analysis 
      suggests that both U12-type AT-AC and U12-type GT-AG introns occurred in 
      Na<sup>+</sup>/H<sup>+</sup> antiporters in a progenitor of animals and 
      plants. <br />
    </p>
    <p align="justify"><strong>Supporting Materials</strong></p>

  <ul style="text-align:left;">
    <li><em><a href="U12.php"> Arabidopsis</a></em><a href="U12.php">U12-type introns</a></li>
    <li><a href="U12_splice_signals.php"><em>Arabidopsis</em> U12-type splice signals</a></li>
    <li><a href="multi_align_nhx.html">Complete multiple alignment of Na<sup>+</sup>/H<sup>+</sup> 
      antiporters</a></li>
  </ul>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>

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eXtensible Genome Data Broker

The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data. Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data.

Project homepage: http://sourceforge.net/projects/xgdb
Programming language(s): JavaScript,Perl,PHP
License: other

  U12.php
  U12.png
  U12_at_ax_acc_new.gif
  U12_at_ax_branch_new.gif
  U12_at_ax_donor_new.gif
  U12_gt_ag_acc_new.gif
  U12_gt_ag_branch_new.gif
  U12_gt_ag_donor_new.gif
  U12_splice_signals.php
  index.php
  ins
  multi_align_nhx.html