Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DkikGB2 Primary Table: refseqRNA Row Count: 25,296 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFH02000053	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	429	`int(10) unsigned`	range
`name`	XM_041774353	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	429	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	429,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFH02000053	0	429	XM_041774353	1000	-	0	429	1	429,	0,
585	AFFH02000099	99	1824	XM_041777247	998	+	99	1824	2	319,363,	0,1362,
585	AFFH02000166	0	851	XM_041776540	1000	-	0	851	1	851,	0,
585	AFFH02000168	88	566	XR_005991046	1000	-	88	88	3	110,156,105,	0,166,373,
585	AFFH02000219	538	3971	XR_005990956	976	-	538	538	5	236,27,140,361,2630,	0,246,299,441,803,
585	AFFH02000219	538	3971	XR_005990957	976	-	538	538	5	236,27,140,361,2630,	0,246,299,441,803,
585	AFFH02000233	2485	3268	XM_041776349	982	+	2592	2980	5	273,113,118,154,54,	0,285,399,574,729,
585	AFFH02000278	190	486	XR_005990774	1000	+	190	190	2	170,47,	0,249,
585	AFFH02000279	0	1011	XM_041774622	964	+	0	1011	4	413,58,62,350,	0,413,599,661,
585	AFFH02000284	0	343	XM_041774624	960	+	0	343	2	247,96,	0,247,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. kikkawai transcripts from the NCBI RefSeq database were aligned against the D. kikkawai assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. kikkawai transcripts were mapped against the D. kikkawai 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_018152535.1.

Description