Schema for RefSeq Genes - BLAT Alignments of NCBI RefSeq Genes

Database: DyakCAF1 Primary Table: refseqRNA Row Count: 30,001 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	750	`int(10) unsigned`	range
`chromEnd`	3293	`int(10) unsigned`	range
`name`	XR_006245117	`varchar(255)`	values
`score`	982	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	750	`int(10) unsigned`	range
`thickEnd`	750	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	5	`int(10) unsigned`	range
`blockSizes`	1626,40,108,313,317,	`longblob`
`chromStarts`	0,1626,1680,1788,2226,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	chr2L	750	3293	XR_006245117	982	-	750	750	5	1626,40,108,313,317,	0,1626,1680,1788,2226,
585	chr2L	750	3292	XR_005560275	984	-	750	750	6	855,681,40,108,313,316,	0,945,1626,1680,1788,2226,
585	chr2L	750	3293	XR_005560274	984	-	750	750	6	886,681,40,108,313,317,	0,945,1626,1680,1788,2226,
585	chr2L	6816	16159	XM_002087329	1000	-	8643	14684	9	1957,109,443,643,106,1192,779,161,295,	0,2020,2463,2968,3877,4040,5290,7784,9048,
585	chr2L	8939	16160	XM_015197872	1000	-	9045	14684	8	129,443,643,106,1192,779,161,296,	0,340,845,1754,1917,3167,5661,6925,
585	chr2L	20845	48858	XM_039371265	1000	-	20962	47705	13	285,199,438,226,194,87,444,47,484,197,557,102,95,	0,349,645,1658,2393,2642,6526,7252,7366,11195,11657,26790,27918,
585	chr2L	20845	54906	XM_039371253	1000	-	20962	47705	14	285,199,438,229,194,87,801,444,47,484,197,557,102,238,	0,349,645,2060,2393,2642,4098,6526,7252,7366,11195,11657,26790,33823,
585	chr2L	20845	61792	XM_039371254	1000	-	20962	47705	14	285,199,438,229,194,87,801,444,47,484,197,557,102,130,	0,349,645,2060,2393,2642,4098,6526,7252,7366,11195,11657,26790,40817,
585	chr2L	20845	48740	XM_039371255	1000	-	20962	47705	14	285,199,438,229,194,87,801,444,47,484,197,557,102,219,	0,349,645,2060,2393,2642,4098,6526,7252,7366,11195,11657,26790,27676,
585	chr2L	20845	48860	XM_039371256	1000	-	20962	47705	14	285,199,438,226,194,87,801,444,47,484,197,557,102,97,	0,349,645,1658,2393,2642,4098,6526,7252,7366,11195,11657,26790,27918,

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

RefSeq Genes (refseqRNA) Track Description


	Description D. yakuba transcripts from the NCBI RefSeq database were aligned against the D. yakuba assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. yakuba transcripts were mapped against the D. yakuba 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_016746365.2.

Description