Description

The RefSeq mRNAs gene track for the 17 Jun 2025 Megachile rotundata/GCF_050947335.1_iyMegRotu1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Data Access

Download GCF_050947335.1_iyMegRotu1.xenoRefGene.gtf.gz GTF file.

Track statistics summary

Total genome size: 613,361,532
Gene count: 4,099
Bases in genes: 42,517,947
Percent genome coverage: % 6.932

Methods

The mRNAs were aligned against the Megachile rotundata/GCF_050947335.1_iyMegRotu1 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 RefSeq
The 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_050947335.1_iyMegRotu1.xenoRefGene.psl
The filtered GCF_050947335.1_iyMegRotu1.xenoRefGene.psl is converted to genePred data to display for this track.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

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