Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DanaCAF1 Primary Table: refseqRNA Row Count: 37,364 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10000	`varchar(255)`	values
`chromStart`	3848	`int(10) unsigned`	range
`chromEnd`	4105	`int(10) unsigned`	range
`name`	XR_004310392	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	3848	`int(10) unsigned`	range
`thickEnd`	3848	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	125,59,	`longblob`
`chromStarts`	0,198,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	scaffold_10000	3848	4105	XR_004310392	1000	-	3848	3848	2	125,59,	0,198,
585	scaffold_10009	4526	5020	XR_004311427	996	-	4526	4526	2	125,296,	0,198,
585	scaffold_10009	4535	4821	XR_004310395	964	-	4535	4535	2	116,97,	0,189,
585	scaffold_10011	1656	2224	XR_006507906	1000	-	1656	1656	4	23,37,107,37,	0,191,346,531,
585	scaffold_10011	1757	2224	XR_006507905	1000	-	1757	1757	4	24,37,107,37,	0,90,245,430,
585	scaffold_10011	1757	2231	XR_006507907	1000	-	1757	1757	4	24,37,107,44,	0,90,245,430,
585	scaffold_10017	1050	2010	XR_004311337	998	-	1050	1050	4	64,143,110,195,	0,449,653,765,
585	scaffold_10039	13726	13932	XR_006508007	962	-	13726	13726	1	206,	0,
585	scaffold_1005	0	1237	XM_032453539	1000	+	0	1181	2	810,369,	0,868,
585	scaffold_10103	340	1383	XM_014903521	990	-	518	1221	3	319,346,325,	0,372,718,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. ananassae transcripts from the NCBI RefSeq database were aligned against the D. ananassae assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. ananassae transcripts were mapped against the D. ananassae 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_017639315.1.

Description