All mouse transcripts sequences were downloaded and combined as a Combined Alternative Splicing Database (CASD).
The shRNAs included Znf179 shRNAs (TRCN0000040979 and TRCN0000040980), which targeted the mouse Znf179 transcript sequences, 5′-GCCGGAAGATCTGTAAGCAAA-3′ (sh_2) and 5′-GATACCGATCTGGGCTATCTA-3′ (sh_3), p35 shRNA (TRCN0000009518), which targeted the mouse p35 transcript sequence, 5′-GACCCACACTATTTCACACAA-3′ (sh_4), and the luciferase control (pLKO.1-shLuc) plasmid constructs were used.
In addition to the human pre-miRNA target genes predicted from human ESTs, we retrieved the sequences of 3' UTRs of mouse and rat genes from the mouse reference gene transcript sequences and rat reference gene transcript sequences (mouse.rna.fna, rat.rna.fna; RefSeq release 3)[ 22].
We repeated the analysis with chimpanzee, mouse and rat transcript sequences.
Mining the SwissProt protein database and the ENSEMBL collection of mouse transcripts (ECMT) for sequences similar to those present in our dataset allowed detection of transcripts from a large number of putative genes.
Next, we directly compared the nucleotide and amino acid sequence of the alternatively spliced mouse transcript to the entire human MCOLN1 genomic sequence and found no significant similarity.
Parsing Spidey result files and incorporating information about transcript length and coding sequence CDS location, we computed the fraction of the mouse transcript length covered by the bank vole sequences, both overall and separately for untranslated regions and CDS.
The UniGene database consists of non-redundant, curated collections of transcript sequences of Arabidopsis, mouse, and human.
This hypothesis is supported by the existence of ESTs in wool and skin from sheep whereas transcript databases of other mammalian species (human, mouse, pig, horse and dog) revealed no similar transcript sequences.
