Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DereCAF1 Primary Table: refseqRNA Row Count: 26,935 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1034	`varchar(255)`	values
`chromStart`	522	`int(10) unsigned`	range
`chromEnd`	701	`int(10) unsigned`	range
`name`	XR_003408280	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	522	`int(10) unsigned`	range
`thickEnd`	522	`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_1034	522	701	XR_003408280	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408322	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408334	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_046930	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408290	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408282	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408325	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408289	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408256	1000	+	522	522	1	179,	0,
585	scaffold_1034	522	701	XR_003408255	1000	+	522	522	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. erecta transcripts from the NCBI RefSeq database were aligned against the D. erecta assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. erecta transcripts were mapped against the D. erecta 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_003286155.1.

Description