RefSeq mRNAs mapped to this assembly (NM_001277276)
Item: NM_001277276
Score: 0
Position: HG999680.1:64697192-64711320
Genomic Size: 14129
Strand: +
View DNA for this feature (GCA_905368555.1/turkey (WU_HG_1 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 exon0,0,0,0,0,0,1,1,2,1,0,2,-1,
Transcript type
gene namePYROXD1
species of origin of the mRNAGallus gallus
Gene type

Links to sequence:

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Go to RefSeq mRNAs track controls


The RefSeq mRNAs gene track for the 26 Mar 2021 Meleagris gallopavo/GCA_905368555.1_MGAL_WU_HG_1.0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,001,818,376
Gene count: 12,910
Bases in genes: 398,861,117
Percent genome coverage: % 39.814

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The mRNAs were aligned against the Meleagris gallopavo/GCA_905368555.1_MGAL_WU_HG_1.0 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_905368555.1_MGAL_WU_HG_1.0.xenoRefGene.psl
The filtered GCA_905368555.1_MGAL_WU_HG_1.0.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 scientists worldwide.


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