The RefSeq mRNAs gene track for the 09 Sep 2019 Hyalella azteca/GCF_000764305.2_Hazt_2.0.2 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCF_000764305.2_Hazt_2.0.2.xenoRefGene.gtf.gz GTF file.
Total genome size: 542,364,171
Gene count: 3,111
Bases in genes: 30,226,413
Percent genome coverage: % 5.573
The mRNAs were aligned against the Hyalella azteca/GCF_000764305.2_Hazt_2.0.2 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_000764305.2_Hazt_2.0.2.xenoRefGene.psl
The filtered GCF_000764305.2_Hazt_2.0.2.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