The RefSeq mRNAs gene track for the 26 Apr 2016 Mus musculus castaneus/GCA_001624445.1_CAST_EiJ_v1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCA_001624445.1_CAST_EiJ_v1.xenoRefGene.gtf.gz GTF file.
Total genome size: 2,653,990,650
Gene count: 21,103
Bases in genes: 999,479,544
Percent genome coverage: % 37.659
The mRNAs were aligned against the Mus musculus castaneus/GCA_001624445.1_CAST_EiJ_v1 genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.
Specifically, the translated blat command is:
blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl where target.fa is one of the chromosome sequence of the genome assembly, and the query.fa is the mRNAs from RefSeqThe resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25 -globalNearBest=0.0100 -minQSize=20
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
all.results.psl GCA_001624445.1_CAST_EiJ_v1.xenoRefGene.psl
The filtered GCA_001624445.1_CAST_EiJ_v1.xenoRefGene.psl is converted to
genePred data to display for this track.
The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779
Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518