RefSeq mRNAs mapped to this assembly (NM_003112)
 
Item: NM_003112
Score: 0
Position: NW_024356505.1:13250278-13277833
Genomic Size: 27556
Strand: -
View DNA for this feature (GCF_014805655.1/ASM1480565v1 Sep. 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 exon-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,1,1,1,1,1,1,1,2,0,-1,
Transcript type
gene nameSP4
species of origin of the mRNAHomo sapiens
Gene type

Links to sequence:

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Go to RefSeq mRNAs track controls


Description

The RefSeq mRNAs gene track for the 30 Sep 2020 Passer montanus/GCF_014805655.1_ASM1480565v1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,039,966,254
Gene count: 12,550
Bases in genes: 386,746,706
Percent genome coverage: % 37.188

Methods

The mRNAs were aligned against the Passer montanus/GCF_014805655.1_ASM1480565v1 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_014805655.1_ASM1480565v1.xenoRefGene.psl
The filtered GCF_014805655.1_ASM1480565v1.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