2021.2.25: mouse mm39 ensembl GTF file not available from UCSC yet. Downloaded from Gencode instead: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/gencode.vM26.annotation.gtf.gz

genome: http://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz
transcriptome: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/gencode.vM26.transcripts.fa.gz
GTF: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/gencode.vM26.annotation.gtf.gz