Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DsuzGB1 Primary Table: refseqRNA Row Count: 30,350 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AWUT01012676	`varchar(255)`	values
`chromStart`	14309	`int(10) unsigned`	range
`chromEnd`	44845	`int(10) unsigned`	range
`name`	XM_036822623	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	14324	`int(10) unsigned`	range
`thickEnd`	44753	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(10) unsigned`	range
`blockSizes`	88,334,142,206,	`longblob`
`chromStarts`	0,7454,7841,30330,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AWUT01012676	14309	44845	XM_036822623	1000	-	14324	44753	4	88,334,142,206,	0,7454,7841,30330,
585	AWUT01012676	21563	44845	XM_017082120	1000	-	21656	44753	4	115,334,142,206,	0,200,587,23076,
585	AWUT01012676	21763	44843	XM_036822618	1000	-	21763	44753	3	325,142,204,	0,387,22876,
585	AWUT01012676	21763	44845	XM_036822622	1000	-	21763	44753	3	334,142,206,	0,387,22876,
585	AWUT01012676	21763	44843	XM_036822617	1000	-	21763	44753	3	334,142,204,	0,387,22876,
585	AWUT01013449	8100	66641	XM_017084180	1000	+	8278	66626	7	265,611,634,193,209,346,83,	0,340,48565,49255,49506,49766,58458,
585	AWUT01013449	8102	60179	XM_036821409	998	+	8278	60072	8	263,611,634,193,209,810,158,114,	0,338,48563,49253,49504,49764,50629,51963,
585	AWUT01013449	8104	60673	XM_036821410	990	+	8278	60564	10	261,611,634,193,209,158,145,126,189,181,	0,336,48561,49251,49502,50627,51764,51961,52145,52388,
585	AWUT01013449	8105	60673	XM_036821411	986	+	8278	60564	6	260,611,145,126,189,181,	0,335,51763,51960,52144,52387,
585	AWUT01013449	8105	60673	XM_017084179	992	+	8278	60564	11	260,611,634,193,209,810,158,145,126,189,181,	0,335,48560,49250,49501,49761,50626,51763,51960,52144,52387,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. suzukii transcripts from the NCBI RefSeq database were aligned against the D. suzukii assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. suzukii transcripts were mapped against the D. suzukii 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_013340165.1.

Description