Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DmirGB2 Primary Table: refseqRNA Row Count: 36,498 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	1925	`int(10) unsigned`	range
`chromEnd`	5083	`int(10) unsigned`	range
`name`	XM_033388030	`varchar(255)`	values
`score`	994	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1943	`int(10) unsigned`	range
`thickEnd`	5083	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	162,394,50,	`longblob`
`chromStarts`	0,2622,3108,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	CM001516	1925	5083	XM_033388030	994	-	1943	5083	3	162,394,50,	0,2622,3108,
585	CM001516	3525	3576	XR_004471185	962	-	3525	3525	1	51,	0,
585	CM001516	4376	5181	XM_033388161	1000	-	4412	5181	2	552,18,	0,787,
585	CM001516	4376	5181	XM_033388158	1000	-	4412	5181	2	552,18,	0,787,
585	CM001516	4381	5181	XM_033388153	1000	-	4412	5181	2	547,18,	0,782,
585	CM001516	4381	5181	XM_033388160	1000	-	4412	5181	2	547,18,	0,782,
585	CM001516	4381	5083	XM_033388154	1000	-	4412	5083	2	560,50,	0,652,
585	CM001516	4381	5181	XM_033388157	1000	-	4412	5181	2	547,18,	0,782,
585	CM001516	4412	4998	XM_033388156	1000	-	4412	4998	2	531,54,	0,532,
585	CM001516	5616	7699	XR_004474212	974	-	5616	5616	6	211,218,230,143,181,148,	0,211,430,768,911,1935,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. miranda transcripts from the NCBI RefSeq database were aligned against the D. miranda assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. miranda transcripts were mapped against the D. miranda 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_003369915.1.

Description