Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DperCAF1 Primary Table: refseqRNA Row Count: 24,235 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	super_0	`varchar(255)`	values
`chromStart`	31789	`int(10) unsigned`	range
`chromEnd`	32592	`int(10) unsigned`	range
`name`	XM_002012702	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	31811	`int(10) unsigned`	range
`thickEnd`	32191	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	217,527,	`longblob`
`chromStarts`	0,276,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	super_0	31789	32592	XM_002012702	1000	+	31811	32191	2	217,527,	0,276,
585	super_0	34388	42941	XM_026984113	1000	-	34774	42841	6	408,351,2535,196,1536,782,	0,465,913,3843,4097,7771,
585	super_0	34388	63039	XM_026984116	1000	-	34774	39998	6	408,351,2535,196,1536,53,	0,465,913,3843,4097,28598,
585	super_0	34388	42936	XM_026984114	1000	-	34774	42841	7	408,351,2535,196,571,839,777,	0,465,913,3843,4097,4794,7771,
585	super_0	34388	42937	XM_026984115	1000	-	34774	42841	6	408,222,2502,196,1536,778,	0,465,913,3843,4097,7771,
585	super_0	34388	42936	XM_002012703	1000	-	34774	42841	6	408,351,2502,196,1536,777,	0,465,913,3843,4097,7771,
585	super_0	53672	63041	XM_026984117	998	-	53819	55119	4	949,4,713,55,	0,949,953,9314,
585	super_0	60224	62371	XM_026984119	978	+	61656	62149	5	107,307,974,80,511,	0,169,476,1502,1636,
585	super_0	60224	62903	XR_003408372	990	+	60224	60224	6	107,307,974,80,409,383,	0,169,476,1502,1636,2296,
585	super_0	63596	65816	XM_002012706	1000	+	63640	65714	2	322,1897,	0,323,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. persimilis transcripts from the NCBI RefSeq database were aligned against the D. persimilis assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. persimilis transcripts were mapped against the D. persimilis 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_003286085.1.

Description