Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DeugGB2 Primary Table: refseqRNA Row Count: 23,815 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02000031	`varchar(255)`	values
`chromStart`	17537	`int(10) unsigned`	range
`chromEnd`	23978	`int(10) unsigned`	range
`name`	XM_017210188	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	18278	`int(10) unsigned`	range
`thickEnd`	23768	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	10	`int(10) unsigned`	range
`blockSizes`	449,254,160,138,491,478,271...	`longblob`
`chromStarts`	0,507,861,1162,1356,1902,37...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFPQ02000031	17537	23978	XM_017210188	1000	+	18278	23768	10	449,254,160,138,491,478,271,155,291,321,	0,507,861,1162,1356,1902,3730,5555,5772,6120,
585	AFPQ02000207	0	450	XM_017229081	990	-	20	340	2	137,257,	0,193,
585	AFPQ02000213	73	912	XM_017212907	982	-	160	832	2	261,266,	0,573,
585	AFPQ02000467	2903	3786	XM_041819793	996	-	2903	3783	2	79,797,	0,86,
585	AFPQ02000467	4208	5401	XR_005993643	994	+	4208	4208	3	432,397,306,	0,434,887,
585	AFPQ02000467	4341	5401	XR_005993642	998	+	4341	4341	3	299,397,306,	0,301,754,
585	AFPQ02000467	4929	5401	XM_041817740	1000	+	4937	5302	2	110,306,	0,166,
585	AFPQ02000534	35	5837	XM_041819438	990	+	2030	5837	24	360,208,55,34,271,68,11,13,138,55,32,3,224,607,7,137,429,86,1077,3,9,105,1232,287,	0,372,581,637,999,1270,1338,1349,1362,1500,1559,1592,1596,1822,2429,2436,2573,3002,3088,4165,4168,4177,4282,5515,
585	AFPQ02000534	964	5837	XM_041819668	988	+	2030	5837	18	341,68,24,138,55,26,6,3,224,106,501,7,137,429,86,568,1231,287,	0,341,409,433,571,630,656,663,667,893,999,1500,1507,1644,2073,2159,3354,4586,
585	AFPQ02000534	1041	5837	XM_041817727	984	+	2030	5837	20	264,68,11,13,121,17,55,25,224,607,7,137,429,86,1077,3,9,105,1232,287,	0,264,332,343,356,477,494,553,590,816,1423,1430,1567,1996,2082,3159,3162,3171,3276,4509,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. eugracilis transcripts from the NCBI RefSeq database were aligned against the D. eugracilis assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. eugracilis transcripts were mapped against the D. eugracilis 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_018153835.1.

Description