Description

The RefSeq mRNAs gene track for the 03 Apr 2018 Neophocaena asiaeorientalis asiaeorientalis/GCA_003031525.1_Neophocaena_asiaeorientalis_V1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Data Access

Download GCA_003031525.1_Neophocaena_asiaeorientalis_V1.xenoRefGene.gtf.gz GTF file.

Track statistics summary

Total genome size: 2,284,611,699
Gene count: 18,726
Bases in genes: 882,580,659
Percent genome coverage: % 38.632

Methods

The mRNAs were aligned against the Neophocaena asiaeorientalis asiaeorientalis/GCA_003031525.1_Neophocaena_asiaeorientalis_V1 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

pslCDnaFilter -minId=0.35 -minCover=0.25  -globalNearBest=0.0100 -minQSize=20 
  -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap 
    all.results.psl GCA_003031525.1_Neophocaena_asiaeorientalis_V1.xenoRefGene.psl

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