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Murray JI
Voelker RB
Henscheid KL
Warf MB
Berglund JA

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Voelker RB
Henscheid KL
Warf MB
Berglund JA
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Identification of motifs that function in the splicing of non-canonical introns

Jill I Murray , Rodger B Voelker , Kristy L Henscheid , M Bryan Warf and J Andrew Berglund

Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon, USA

author email corresponding author email

Genome Biology 2008, 9:R97doi:10.1186/gb-2008-9-6-r97


Published:	12 June 2008

Subject areas: Genome studies

Additional files

Additional data file 1:

Table listing the count and the probability of occurrence (using a sliding window) for all pentamers found in the sequences reported in Singh et al. [27] and both SELEX experiments reported in Banerjee et al. [39].

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Additional data file 2:

Associated statistics and listing of n-mers (4-7 nucleotides) determined to be enriched in the 50 nucleotide region upstream of weak PY tracts from GC-rich introns.

Format: PDF Size: 73KB Download file

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Additional data file 3:

Associated statistics and listing of n-mers (4-7 nucleotides) determined to be enriched in the 50 nucleotide region upstream of weak PY tracts from AT-rich introns.

Format: PDF Size: 40KB Download file

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Additional data file 4:

Listing of all clusters derived from n-mers enriched in the 50 nucleotide region upstream of weak PY tracts from GC-rich introns. Included are the individual n-mers and associated statistics used to produce each motif.

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Additional data file 5:

Listing of all clusters derived from n-mers enriched in the 50 nucleotide region upstream of weak PY tracts from AT-rich introns. Included are the individual n-mers and associated statistics used to produce each motif.

Format: PDF Size: 28KB Download file

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Additional data file 6:

The Z-scores for enrichment of all 4-7 nucleotide n-mers in the intronic region upstream (-80 to -30 relative to the acceptor splice-junction) of PY tracts with low S₆₅scores for short (<200 nucleotide) introns is plotted versus long (≥ 200 nucleotide) introns. (a) Data for GC-rich introns. (b) Data for AT-rich introns.

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Additional data file 7:

The portion of the sequence corresponding to the -80 to -30 region matching one or more of the n-mers enriched in the same region for introns with weak PY tracts (Additional data files 2 and 3) was determined. These values (referred to as the percent coverage) were binned as indicated along the x-axis.

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