The RefSeq mRNAs gene track for the 16 Jan 2018 Oncorhynchus tshawytscha/GCF_002872995.1_Otsh_v1.0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCF_002872995.1_Otsh_v1.0.xenoRefGene.gtf.gz GTF file.
Total genome size: 2,425,709,133
Gene count: 27,462
Bases in genes: 638,352,913
Percent genome coverage: % 26.316
The mRNAs were aligned against the Oncorhynchus tshawytscha/GCF_002872995.1_Otsh_v1.0 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 GCF_002872995.1_Otsh_v1.0.xenoRefGene.psl
The filtered GCF_002872995.1_Otsh_v1.0.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