Applied methods to find introns in homologous genes as well as new ones in the 7 related species.



BACK to 'Hemiascomycetous Yeast Spliceosomal Introns'


1. Search for S. cerevisiae-like introns

S. cerevisiae introns
(MIPS, YIDB, ARES, Génolevures)
252 genes / 260 introns
<<====>> S. cerevisiae homologues
9764 coding sequences,
either full length or partial

S. cerevisiae homologues, identified through BLAST comparisons, were collected in each of the seven yeast species, and compared to an updated and non-redundant catalogue of S. cerevisiae genes containing intron.

A) BLAST output:
Blast output


B) BLAST alignment:
Blast alignment


C) Protein translations (SS = Splicing Sites; BP = Branching Site):
protein translation

2. Search for « specific » introns, visual scrutinization

The BLAST outputs were also manually scrutinized to detect any abrupt stop in homology, as well as a gap occuring between two conserved amino acid sequences of a same protein.

3. Search for intron features

A catalogue of known hemiascomycetous yeast splicing signals was then used as bait to screen the batch of selected coding sequences, and to validate or not the presence of an intron.

Yeast speciesNumber of genes
with introns
5' motifBranch motif3' motif
GTATGTTAC TAACTAG
GTACGTCAC TAACCAG
GTATGAGAC TAACAAG
S.cerevisiaean = 260 intronsGTATGCTGC TAAC
n' = 252 genesGCATGTAAC TAAC
GTAAGTTAT TAAC
GTCAGTAAT TAAC
GTTCGT
GTGAGTTAC TAACCAG
Y. lipolyticabn=17 intronsGTAAGTAAC TAACTAG
n' = 13 genesGTGGGTCGC TAAC
ATC TAAC

a Compilation of the ARES lab intron database Spingola M. et al. 1999. RNA Feb;5(2):221-34 and Génolevures.
b Compilation of intron sequences available at NCBI (release of June 2001).
Last modified: Tue Feb 10 11:14:44 CET 2004