Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DserGB1 Primary Table: refseqRNA Row Count: 23,600 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	MTTC01000001	`varchar(255)`	values
`chromStart`	9471	`int(10) unsigned`	range
`chromEnd`	13930	`int(10) unsigned`	range
`name`	XM_020946020	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	9471	`int(10) unsigned`	range
`thickEnd`	13930	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	106,524,114,	`longblob`
`chromStarts`	0,1502,4345,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	MTTC01000001	9471	13930	XM_020946020	1000	+	9471	13930	3	106,524,114,	0,1502,4345,
585	MTTC01000001	20880	21330	XM_020957106	1000	+	20880	21330	1	450,	0,
585	MTTC01000002	1360	2124	XM_020962249	1000	+	1360	2124	2	455,247,	0,517,
585	MTTC01000002	2613	3540	XM_020959123	1000	-	2613	3540	1	927,	0,
585	MTTC01000002	2613	3540	XM_020942472	1000	-	2613	3540	1	927,	0,
585	MTTC01000002	3569	4317	XM_020959124	1000	+	3569	4317	2	13,554,	0,194,
585	MTTC01000002	3569	4317	XM_020943631	1000	+	3569	4317	2	13,554,	0,194,
585	MTTC01000002	10932	11421	XM_020944858	1000	+	10932	11421	1	489,	0,
585	MTTC01000002	10932	11421	XM_020959126	1000	+	10932	11421	1	489,	0,
585	MTTC01000002	11435	12290	XM_020959127	1000	+	11435	12290	1	855,	0,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. serrata transcripts from the NCBI RefSeq database were aligned against the D. serrata assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. serrata transcripts were mapped against the D. serrata 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_002093755.1.

Description