The RefSeq mRNAs gene track for the 16 Mar 2019 Denticeps clupeoides/GCF_900700375.1_fDenClu1.1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Total genome size: 567,401,054
Gene count: 16,567
Bases in genes: 206,599,710
Percent genome coverage: % 36.412
The mRNAs were aligned against the Denticeps clupeoides/GCF_900700375.1_fDenClu1.1 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_900700375.1_fDenClu1.1.xenoRefGene.pslThe filtered GCF_900700375.1_fDenClu1.1.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.
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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
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