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BIOINF 15-046: U6 snRNA Intron Insertion Occurred Multiple Times During Fungi Evolution
Taxonomic Tree
A taxonomic classification of all 147 fungal organisms that were used in our publication can be found here: Taxonomic TreeAlignments
Alignments of precursor and mature snRNA sequences in clustal format and stockholm format can be found here:(only one U6 gene per species, for visiblity reasons) Lineage specific fasta files, alignments, and gene structures of all U6 sequence that have been retrieved during our analysis can be accessed in the following table:
Kingdom | Phylum | Subphylum | Class | Precursor Fasta | Precursor Alignment | Precursor gene structure |
---|---|---|---|---|---|---|
Fungi | Microsporidia | fasta | aln|stk | ps|png | ||
Fungi incertae sedis | Mucoromycotina | fasta | aln|stk | ps|png | ||
Chytridiomycota | fasta | aln|stk | ps|png | |||
Blastocladiomycota | fasta | aln|stk | ps|png | |||
Basidiomycota | fasta | aln|stk | ps|png | |||
Ascomycota | Taphrinomycotina | fasta | aln|stk | ps|png | ||
Saccharomycotina | fasta | aln|stk | ps|png | |||
Pezizomycotina | Dothideomycetes | fasta | aln|stk | ps|png | ||
Eurotiomycetes | fasta | aln|stk | ps|png | |||
Leotiomycetes | fasta | aln|stk | ps|png | |||
Sordariomycetes | fasta | aln|stk | ps|png |
Cross-validation with published RNA-seq data
- Fusarium graminearum
The Fusarium graminearum Genome Database and published RNA-seq tracks can be found here . Reference: Wong et al.
Overlap of U6.1 gene with RNA-seq reads showing the excision of all three canonical GT-AG introns: fgr.U6.1.png
Overlap of the intronless U6.2 gene with RNA-seq reads: fgr.U6.2.png - Schizosaccharomyce pombe
The Schizosaccharomyces pombe Genome Browser and the RNA-seq tracks published by Marguerat et al. can be found here.
Overlap of different RNA-seq experiments with the annotated spo.U6.1 gene: spo.U6.1.png
- Trichoderme reesei
The mapped short read archive published by Ries et al. can be accessed here.
Overlap of mapped reads of sample GSM1088351 with the identified tre.U6.1 gene: tre.U6.1.png