source for genome: UCSC mm10;
transcriptome (both original version and shortHeader version): Gencode mm10 vM25;
unspliced transcriptome: ensGene gtf from UCSC mm10, extract "transcripts" by Matlab, and use bedtools to getfasta from UCSC mm10 genome with transcripts gtf; when using bedtools, gtf coordinates (1-based) have been converted to bed coordinates (0-based).