Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DbiaGB2 Primary Table: refseqRNA Row Count: 27,117 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	791	`int(10) unsigned`	range
`chromEnd`	2597	`int(10) unsigned`	range
`name`	XR_006368561	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	791	`int(10) unsigned`	range
`thickEnd`	791	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	116,37,86,	`longblob`
`chromStarts`	0,180,1720,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFD02000037	791	2597	XR_006368561	1000	-	791	791	3	116,37,86,	0,180,1720,
585	AFFD02000037	791	2424	XR_006368558	1000	-	791	791	3	116,37,100,	0,180,1533,
585	AFFD02000037	791	2583	XR_001768713	998	-	791	791	3	116,37,370,	0,180,1422,
585	AFFD02000037	791	2596	XR_006368318	1000	-	791	791	3	116,37,85,	0,180,1720,
585	AFFD02000037	791	2519	XR_001768714	1000	-	791	791	3	116,37,195,	0,180,1533,
585	AFFD02000037	791	2283	XR_006368112	1000	-	791	791	3	116,37,70,	0,180,1422,
585	AFFD02000037	791	2298	XR_006368559	996	-	791	791	3	116,37,205,	0,180,1302,
585	AFFD02000037	791	2297	XR_006368560	1000	-	791	791	3	116,37,84,	0,180,1422,
585	AFFD02000037	837	2251	XR_006368257	1000	-	837	837	3	70,37,38,	0,134,1376,
585	AFFD02000037	837	2123	XR_006368258	1000	-	837	837	3	70,37,30,	0,134,1256,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. biarmipes transcripts from the NCBI RefSeq database were aligned against the D. biarmipes assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. biarmipes transcripts were mapped against the D. biarmipes 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_025231255.1.

Description