RefSeq mRNAs mapped to this assembly (NM_001017116)
 
Item: NM_001017116
Score: 0
Position: CM026039.1:46715983-46738332
Genomic Size: 22350
Strand: -
View DNA for this feature (GCA_014839835.1/downy woodpecker (VGP 2020))

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 exon2,2,2,1,1,0,0,
Transcript type
gene nameacer2
species of origin of the mRNAXenopus tropicalis
Gene type

Links to sequence:

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Go to RefSeq mRNAs track controls


Description

The RefSeq mRNAs gene track for the 02 Oct 2020 Dryobates pubescens/GCA_014839835.1_bDryPub1.pri genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,187,956,536
Gene count: 12,405
Bases in genes: 453,107,337
Percent genome coverage: % 38.142

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Methods

The mRNAs were aligned against the Dryobates pubescens/GCA_014839835.1_bDryPub1.pri 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_014839835.1_bDryPub1.pri.xenoRefGene.psl
The filtered GCA_014839835.1_bDryPub1.pri.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