The RefSeq mRNAs gene track for the 14 Jun 2024 Anser cygnoides/GCF_040182565.1_Taihu_goose_T2T_genome genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCF_040182565.1_Taihu_goose_T2T_genome.xenoRefGene.gtf.gz GTF file.
Total genome size: 1,215,354,515
Gene count: 13,715
Bases in genes: 444,625,218
Percent genome coverage: % 36.584
The mRNAs were aligned against the Anser cygnoides/GCF_040182565.1_Taihu_goose_T2T_genome 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 RefSeqThe resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25 -globalNearBest=0.0100 -minQSize=20
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
all.results.psl GCF_040182565.1_Taihu_goose_T2T_genome.xenoRefGene.psl
The filtered GCF_040182565.1_Taihu_goose_T2T_genome.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