RefSeq mRNAs Track Settings
 
RefSeq mRNAs mapped to this assembly   (All RNA and Transcriptome tracks)

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Label: RefSeq accession id    gene name    species of origin of the mRNA   

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Description

The RefSeq mRNAs gene track for the 28 Jun 2020 Plasmodium sp. DRC-Itaito/GCA_900257145.2_Plasmodium_billcollinsi genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Data Access

Download GCA_900257145.2_Plasmodium_billcollinsi.xenoRefGene.gtf.gz GTF file.

Track statistics summary

Total genome size: 21,914,523
Gene count: 303
Bases in genes: 399,676
Percent genome coverage: % 1.824

Methods

The mRNAs were aligned against the Plasmodium sp. DRC-Itaito/GCA_900257145.2_Plasmodium_billcollinsi 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 GCA_900257145.2_Plasmodium_billcollinsi.xenoRefGene.psl
The filtered GCA_900257145.2_Plasmodium_billcollinsi.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