Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DpseGB3 Primary Table: refseqRNA Row Count: 32,452 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	653	`int(10) unsigned`	range
`name`	XM_002132166	`varchar(255)`	values
`score`	994	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	557	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	477,112,	`longblob`
`chromStarts`	0,541,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	CH379058	0	653	XM_002132166	994	-	0	557	2	477,112,	0,541,
585	CH379058	10187	65619	XR_001450854	986	+	10187	10187	5	49,26,91,257,237,	0,38354,54723,54880,55195,
585	CH379058	17024	22879	XM_001357136	986	-	17120	22628	4	5478,123,52,124,	0,5482,5667,5731,
585	CH379058	26754	27658	XM_033379706	970	-	26783	27438	4	185,168,190,237,	0,246,476,667,
585	CH379058	45449	46186	XM_002132168	974	+	45592	45945	3	146,110,347,	0,211,390,
585	CH379058	57116	58564	XM_004444541	994	+	57285	58480	12	209,397,311,65,9,70,46,46,36,22,13,31,	0,263,725,1098,1164,1174,1247,1296,1343,1380,1403,1417,
585	CH379058	58713	59522	XM_015179748	998	+	58811	59477	3	186,352,139,	0,259,670,
585	CH379058	59448	61556	XM_015179749	986	+	59479	61516	1	2108,	0,
585	CH379058	61488	64858	XM_002132169	994	-	61562	64766	1	3370,	0,
585	CH379058	67394	68243	XM_033379991	964	-	67512	68030	4	286,121,67,238,	0,342,544,611,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. pseudoobscura transcripts from the NCBI RefSeq database were aligned against the D. pseudoobscura assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. pseudoobscura transcripts were mapped against the D. pseudoobscura 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_009870125.1.

Description