The RefSeq mRNAs gene track for the 01 Feb 2024 Eleginops maclovinus/GCF_036324505.1_JC_Emac_rtc_rv5 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCF_036324505.1_JC_Emac_rtc_rv5.xenoRefGene.gtf.gz GTF file.
Total genome size: 606,306,633
Gene count: 14,986
Bases in genes: 216,864,538
Percent genome coverage: % 35.768
The mRNAs were aligned against the Eleginops maclovinus/GCF_036324505.1_JC_Emac_rtc_rv5 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_036324505.1_JC_Emac_rtc_rv5.xenoRefGene.psl
The filtered GCF_036324505.1_JC_Emac_rtc_rv5.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