Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DvirCAF1 Primary Table: refseqRNA Row Count: 35,261 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10001	`varchar(255)`	values
`chromStart`	148	`int(10) unsigned`	range
`chromEnd`	327	`int(10) unsigned`	range
`name`	XR_004303187	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	148	`int(10) unsigned`	range
`thickEnd`	148	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	179,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10001	148	327	XR_004303187	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303206	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303201	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303183	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303163	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_049490	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303200	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303197	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303181	1000	+	148	148	1	179,	0,
585	scaffold_10001	148	327	XR_004303184	1000	+	148	148	1	179,	0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RefSeq Genes (refseqRNA) Track Description


	Description D. virilis transcripts from the NCBI RefSeq database were aligned against the D. virilis assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. virilis transcripts were mapped against the D. virilis genome assembly using BLAT with the following parameters: -q=rna -fine -minScore=20 -stepSize=5 The transcript alignments are analyzed by pslReps using the following parameter: -minCover=0.15 -minAli=0.98 -nearTop=0.001 The alignments are then filtered by pslCDnaFilter using the following parameters: -minId=0.95 -minCover=0.15 -localNearBest=0.001 \ -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap References Kent WJ. BLAT — the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. The transcripts were obtained from the NCBI FTP site under the RefSeq assembly accession number GCF_003285735.1.

Description