The RefSeq mRNAs gene track for the 19 Dec 2012 Pneumocystis jirovecii/GCA_000333975.2_ASM33397v2 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCA_000333975.2_ASM33397v2.xenoRefGene.gtf.gz GTF file.
Total genome size: 8,176,364
Gene count: 810
Bases in genes: 992,410
Percent genome coverage: % 12.138
The mRNAs were aligned against the Pneumocystis jirovecii/GCA_000333975.2_ASM33397v2 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_000333975.2_ASM33397v2.xenoRefGene.psl
The filtered GCA_000333975.2_ASM33397v2.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