Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DsimGB2 Primary Table: refseqRNA Row Count: 29,275 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM002910	`varchar(255)`	values
`chromStart`	4002	`int(10) unsigned`	range
`chromEnd`	12681	`int(10) unsigned`	range
`name`	XM_016179293	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	5294	`int(10) unsigned`	range
`thickEnd`	11255	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	9	`int(10) unsigned`	range
`blockSizes`	1422,109,443,643,106,1180,7...	`longblob`
`chromStarts`	0,1485,1856,2371,3579,3754,...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	CM002910	4002	12681	XM_016179293	1000	-	5294	11255	9	1422,109,443,643,106,1180,779,160,279,	0,1485,1856,2371,3579,3754,4992,7169,8400,
585	CM002910	4002	12681	XM_016179292	1000	-	5294	11255	9	1422,109,443,643,106,1192,779,160,279,	0,1485,1856,2371,3579,3742,4992,7169,8400,
585	CM002910	13064	16466	XM_016179291	1000	-	13155	16344	5	860,193,880,282,527,	0,923,1174,2109,2875,
585	CM002910	13064	16466	XM_039291190	1000	-	13155	16344	6	619,160,193,880,282,527,	0,700,923,1174,2109,2875,
585	CM002910	13064	16181	XM_039291191	1000	-	13155	16181	5	860,193,880,282,81,	0,923,1174,2109,3036,
585	CM002910	13064	16466	XM_039291192	1000	-	13155	16344	6	860,193,96,385,282,527,	0,923,1174,1669,2109,2875,
585	CM002910	13986	16466	XM_039291193	1000	-	14125	16344	4	194,890,282,527,	0,242,1187,1953,
585	CM002910	16583	46103	XM_016179280	1000	-	17728	44895	14	1313,199,438,226,194,87,450,47,193,2547,197,557,102,169,	0,1388,1677,2484,3201,3450,8742,9475,9645,10666,13451,14171,28242,29351,
585	CM002910	16583	46930	XM_039291180	1000	-	17728	44895	14	1313,199,438,226,194,87,2877,47,493,2547,197,557,102,996,	0,1388,1677,2484,3201,3450,5264,9475,9645,10666,13451,14171,28242,29351,
585	CM002910	16583	46039	XM_016179284	1000	-	17728	44895	12	1313,199,438,226,194,87,47,493,197,557,102,105,	0,1388,1677,2484,3201,3450,9475,9645,13451,14171,28242,29351,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. simulans transcripts from the NCBI RefSeq database were aligned against the D. simulans assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. simulans transcripts were mapped against the D. simulans 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_016746395.2.

Description