Schema for RefSeq mRNAs - RefSeq mRNAs mapped to this assembly
  Database: hub_32_GCF_000337955.1    Primary Table: hub_32_xenoRefGene Data last updated: 2023-01-02
Big Bed File: https://hgdownload.soe.ucsc.edu/hubs/GCF/000/337/955/GCF_000337955.1/bbi/GCF_000337955.1_F_peregrinus_v1.0.xenoRefGene.bb
Item Count: 12,670
Format description: bigGenePred gene models
fieldexampledescription
chromNC_000878.1Reference sequence chromosome or scaffold
chromStart1417Start position in chromosome
chromEnd2537End position in chromosome
nameNM_001195073.3RefSeq accession id
score0Score (0-1000)
strand++ or - for strand
thickStart2104Start of where display should be thick (start codon)
thickEnd2179End of where display should be thick (stop codon)
reserved0RGB value (use R,G,B string in input file)
blockCount4Number of blocks
blockSizes118,18,245,145,Comma separated list of block sizes
chromStarts0,471,544,975,Start positions relative to chromStart
name2Alternative/human readable name
cdsStartStatnoneStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatnoneStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames-1,-1,0,-1,Exon frame {0,1,2}, or -1 if no frame for exon
typeTranscript type
geneNameNM_001195073.3gene name
geneName2species of origin of the mRNA
geneTypeGene type

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneType
NC_000878.114172537NM_001195073.30+2104217904118,18,245,145,0,471,544,975,nonenone-1,-1,0,-1,NM_001195073.3
NC_000878.189659511NM_126741.20+8965951101546,0,nonenone0,NM_126741.2

RefSeq mRNAs (hub_32_xenoRefGene) Track Description
 

Description

The RefSeq mRNAs gene track for the 05 Feb 2013 Falco peregrinus/GCF_000337955.1_F_peregrinus_v1.0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,171,973,431
Gene count: 12,670
Bases in genes: 399,707,431
Percent genome coverage: % 34.106

Methods

The mRNAs were aligned against the Falco peregrinus/GCF_000337955.1_F_peregrinus_v1.0 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_000337955.1_F_peregrinus_v1.0.xenoRefGene.psl
The filtered GCF_000337955.1_F_peregrinus_v1.0.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