RefSeq mRNAs mapped to this assembly (NM_001039280.2)
  NCBI Nucleotide database: NM_001039280.2

NCBI Nucleotide database: NM_001039280.2
Item: NM_001039280.2
Score: 0
Position: NW_010184745.1:148809-446752
Genomic Size: 297944
Strand: -
View DNA for this feature (GCF_000695765.1/ASM69576v1 Jun. 2014)

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 exon-1,1,1,0,0,0,0,0,1,1,1,2,1,0,0,1,0,0,1,2,2,2,2,1,1,0,
Transcript type
gene nameNM_001039280.2
species of origin of the mRNA
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 02 Jun 2014 Mesitornis unicolor/GCF_000695765.1_ASM69576v1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,087,290,853
Gene count: 12,208
Bases in genes: 194,590,464
Percent genome coverage: % 17.897

Methods

The mRNAs were aligned against the Mesitornis unicolor/GCF_000695765.1_ASM69576v1 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_000695765.1_ASM69576v1.xenoRefGene.psl
The filtered GCF_000695765.1_ASM69576v1.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