Worm Breeder's Gazette 11(1): 27

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Information Contents of C. elegans Splice Sites Vary with Intron Length

Chris Fields

Figure 1

Information contents of splice sites from a data set of 125 C.  
elegans introns have been analyzed using the method of Schneider et al.
(1986).  Regions from 20 bases upstream to 40 bases downstream of 5' 
splice sites, and from 40 bases upstream to 20 bases downstream of 3' 
splice sites were analyzed.  The distribution of information content 
as a function of position for the entire data set is very similar to 
that reported last year (WBG 10(3): 65-66) for a 71 intron data set.  
C.  elegans differs from most higher eukaryotes studied thus far in 
having many (>50%) introns shorter than 75 bases (Blumenthal and 
Thomas, 1988; Hawkins, 1988).  Figure 1 shows the information contents 
of splice sites from introns with lengths greater than (upper plot) or 
less than (lower plot) 75 bases.  The information content for each 
position is calculated as the log(2) of the difference, at that 
position, of the observed base frequencies from equal base frequencies;
the slightly higher information content between the splice sites 
reflects the preference for A+T of C.  elegans introns.  
The information contents of 3' splice sites of introns in the two 
size classes are very similar.  The information contents of the 5' 
splice sites are, however, strikingly different.  Positions 4, 5, and 
6 in the 5' splice sites of long introns encode a total of 
approximately 1 bit more information than the corresponding positions 
in short introns.  While the significance of this difference is not 
known, it suggests that the binding constant between U1 snRNP and the 
5' splice site may vary significantly as a function of intron length 
in C.  elegans.[See Figure 1]

Figure 1