RefSeq mRNAs mapped to this assembly (NM_001205022)
 
Item: NM_001205022
Score: 0
Position: LR991019.1:12517702-12518894
Genomic Size: 1193
Strand: +
View DNA for this feature (GCA_905163495.1/ilCosTrap1.1 Jan. 2021)

Alternative/human readable name
Status of CDS start annotation (none, unknown, incomplete, or complete)none
Status of CDS end annotation (none, unknown, incomplete, or complete)none
Exon frame {0,1,2}, or -1 if no frame for exon0,0,0,
Transcript type
gene nameLOC100169349
species of origin of the mRNAAcyrthosiphon pisum
Gene type

Links to sequence:

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Description

The RefSeq mRNAs gene track for the 28 Jan 2021 Cosmia trapezina/GCA_905163495.1_ilCosTrap1.1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 825,187,538
Gene count: 5,024
Bases in genes: 104,014,094
Percent genome coverage: % 12.605

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Methods

The mRNAs were aligned against the Cosmia trapezina/GCA_905163495.1_ilCosTrap1.1 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_905163495.1_ilCosTrap1.1.xenoRefGene.psl
The filtered GCA_905163495.1_ilCosTrap1.1.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