Description

The RefSeq mRNAs gene track for the 01 Apr 2021 Ambystoma mexicanum/GCA_002915635.3_AmbMex60DD genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Data Access

Download GCA_002915635.3_AmbMex60DD.xenoRefGene.gtf.gz GTF file.

Track statistics summary

Total genome size: 28,206,905,576
Gene count: 16,280
Bases in genes: 6,453,680,767
Percent genome coverage: % 22.880

Methods

The mRNAs were aligned against the Ambystoma mexicanum/GCA_002915635.3_AmbMex60DD 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_002915635.3_AmbMex60DD.xenoRefGene.psl
The filtered GCA_002915635.3_AmbMex60DD.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