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HCDiff callings presume at least three reads with the variant with both forward and reverse reads included; alternatively the quality scores at the variable positions must be over 20 (or over 30 if a homopolymer of five or more bases is involved).
Here, we show that DNA methylation is significantly enriched in included alternatively spliced exons (ASEs) as compared with excluded ASEs.
In all models (OLS and Quantile Regression) renal function was included alternatively as a continuous (eGFR) or categorical variable.
While the last two exons are used in all known isoforms, the first three exons are included alternatively within the four isoforms drep-2-RA to -RD.
Dynactin4 from Homo sapiens is encoded in 14 exons on chromosome 5. Exon 6 ("QHTIHVV") is a differentially included alternatively spliced exon.
These included alternatively spliced genes such as longitudinals lacking (lola) (Neumüller et al., 2011), but also many genes for which tissue-specific alternative splicing has not been described.
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H3K36me3 levels showed enrichments which reflected exon usage, with frequently included alternatively-spliced exons having higher modification levels than infrequently included ones (Supplementary Figure S16).
All CDSs, including alternatively spliced forms, were considered for estimation of the average and median CDS lengths.
Gene annotation of these sequences predicted 87 putative genes, including alternatively splicing transcript forms.
Normalization of the cDNA library led to the enrichment of rare transcripts in U. vulgaris, including alternatively spliced mRNAs.
The Arabidopsis and rice proteome data include alternatively splicing variants, while all the other proteomes do not.
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