RefSeq mRNAs mapped to this assembly (NM_032806)
 
Item: NM_032806
Score: 0
Position: NW_012133857v1:9745914-9772770
Genomic Size: 26857
Strand: -
View DNA for this feature (GCF_000956105.1/Coquerel's sifaka 6110/Marcella (2015 refseq))

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,-1,0,-1,-1,
Transcript type
gene namePOMGNT2
species of origin of the mRNAHomo sapiens
Gene type

Links to sequence:

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Description

The RefSeq mRNAs gene track for the 23 Mar 2015 Propithecus coquereli/GCF_000956105.1_Pcoq_1.0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 2,798,152,141
Gene count: 19,338
Bases in genes: 996,031,489
Percent genome coverage: % 35.596

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Methods

The mRNAs were aligned against the Propithecus coquereli/GCF_000956105.1_Pcoq_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 GCF_000956105.1_Pcoq_1.0.xenoRefGene.psl
The filtered GCF_000956105.1_Pcoq_1.0.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