Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DtakGB2 Primary Table: refseqRNA Row Count: 14,977 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02000001	`varchar(255)`	values
`chromStart`	5617	`int(10) unsigned`	range
`chromEnd`	7196	`int(10) unsigned`	range
`name`	XR_001769870	`varchar(255)`	values
`score`	996	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	5617	`int(10) unsigned`	range
`thickEnd`	5617	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	5	`int(10) unsigned`	range
`blockSizes`	77,19,50,69,124,	`longblob`
`chromStarts`	0,1181,1263,1386,1455,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFI02000001	5617	7196	XR_001769870	996	+	5617	5617	5	77,19,50,69,124,	0,1181,1263,1386,1455,
585	AFFI02000009	19765	20199	XM_017144793	968	+	19833	20195	2	218,139,	0,295,
585	AFFI02000009	21249	25710	XM_017143581	968	+	21249	25481	6	72,135,360,194,112,102,	0,2820,3035,4046,4247,4359,
585	AFFI02000021	1850	1957	XR_006412452	1000	+	1850	1850	1	107,	0,
585	AFFI02000021	1850	1957	XR_006412575	1000	+	1850	1850	1	107,	0,
585	AFFI02000021	1850	1957	XR_006412574	1000	+	1850	1850	1	107,	0,
585	AFFI02000021	1850	1957	XR_006412573	1000	+	1850	1850	1	107,	0,
585	AFFI02000021	5215	8367	XM_017147192	992	-	5215	8363	5	1103,153,420,339,215,	0,1165,1732,2241,2937,
585	AFFI02000021	10014	17051	XM_017148396	988	+	10218	16399	4	177,914,594,532,	0,178,5911,6505,
585	AFFI02000034	13892	16718	XM_044392841	976	+	13892	16718	2	2618,207,	0,2619,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. takahashii transcripts from the NCBI RefSeq database were aligned against the D. takahashii assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. takahashii transcripts were mapped against the D. takahashii 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_018152695.1.

Description