Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DgriCAF1 Primary Table: refseqRNA Row Count: 22,952 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10030	`varchar(255)`	values
`chromStart`	5474	`int(10) unsigned`	range
`chromEnd`	22595	`int(10) unsigned`	range
`name`	XM_043215799	`varchar(255)`	values
`score`	996	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	5624	`int(10) unsigned`	range
`thickEnd`	22528	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	17	`int(10) unsigned`	range
`blockSizes`	224,373,179,247,99,288,102,...	`longblob`
`chromStarts`	0,1276,1734,2905,3222,3377,...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10030	5474	22595	XM_043215799	996	+	5624	22528	17	224,373,179,247,99,288,102,209,164,127,206,218,225,225,158,118,163,	0,1276,1734,2905,3222,3377,3736,9665,9931,10280,11095,11359,11633,11920,16281,16781,16958,
585	scaffold_10030	5930	22595	XM_043215800	996	+	5970	22528	17	96,373,179,247,99,288,102,209,164,127,206,218,225,225,158,118,163,	0,820,1278,2449,2766,2921,3280,9209,9475,9824,10639,10903,11177,11464,15825,16325,16502,
585	scaffold_10030	25524	26756	XM_043215792	1000	-	26755	26756	1	1232,	0,
585	scaffold_10032	1	1091	XM_043215420	984	-	1	1091	4	21,20,38,1005,	0,22,47,85,
585	scaffold_10066	177	936	XM_001997918	1000	+	316	679	3	130,127,434,	0,138,325,
585	scaffold_10069	539	930	XR_004365462	1000	+	539	539	3	26,129,61,	0,67,330,
585	scaffold_10075	990	1480	XM_043216292	1000	-	1030	1444	1	490,	0,
585	scaffold_10086	0	3207	XM_043214387	996	-	0	3207	2	1056,751,	0,2456,
585	scaffold_10090	7	586	XM_001998033	998	-	7	586	1	579,	0,
585	scaffold_10096	2305	5655	XR_006246861	978	-	2305	2305	3	127,109,188,	0,2989,3162,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. grimshawi transcripts from the NCBI RefSeq database were aligned against the D. grimshawi assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. grimshawi transcripts were mapped against the D. grimshawi 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_018153295.1.

Description