The RefSeq mRNAs gene track for the 09 Jul 2016 Theobroma cacao/GCF_000208745.1_Criollo_cocoa_genome_V2
genome assembly displays translated blat alignments of vertebrate and
invertebrate mRNA in
Track statistics summary
Total genome size: 324,879,930
Gene count: 14,294
Bases in genes: 62,700,500
Percent genome coverage: % 19.300
Please note, the name searching system is not completely case insensitive.
When in doubt, enter search names in all lower case to find gene names.
The mRNAs were aligned against the Theobroma cacao/GCF_000208745.1_Criollo_cocoa_genome_V2 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
The filtered GCF_000208745.1_Criollo_cocoa_genome_V2.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
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.
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.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
PMID: 14681350; PMC: PMC308779
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518