RefSeq mRNAs mapped to this assembly (NM_117090)
  NCBI Nucleotide database: NM_117090

NCBI Nucleotide database: NM_117090
Item: NM_117090
Score: 0
Position: NW_006256909.1:7249329-7251693
Genomic Size: 2365
Strand: -
View DNA for this feature (GCF_000478725.1/Eutsalg1_0 Nov. 2013)

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 exon1,2,2,1,1,1,2,0,
Transcript type
gene nameT9A4.9
species of origin of the mRNAArabidopsis thaliana
Gene type

Links to sequence:

Data schema/format description and download

Go to RefSeq mRNAs track controls

Description

The RefSeq mRNAs gene track for the 05 Nov 2013 Eutrema salsugineum/GCF_000478725.1_Eutsalg1_0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Data Access

Download GCF_000478725.1_Eutsalg1_0.xenoRefGene.gtf.gz GTF file.

Track statistics summary

Total genome size: 243,110,105
Gene count: 21,851
Bases in genes: 75,457,679
Percent genome coverage: % 31.038

Methods

The mRNAs were aligned against the Eutrema salsugineum/GCF_000478725.1_Eutsalg1_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 GCF_000478725.1_Eutsalg1_0.xenoRefGene.psl
The filtered GCF_000478725.1_Eutsalg1_0.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