Schema for D. mel Transcripts - BLAT Alignment of D. melanogaster Transcripts

Database: DmirGB2 Primary Table: DmelTranscriptsBLAT Row Count: 29,665 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	15218	`int(10) unsigned`	range
`chromEnd`	16790	`int(10) unsigned`	range
`name`	Cyp311a1-RB	`varchar(255)`	values
`score`	490	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	15218	`int(10) unsigned`	range
`thickEnd`	16790	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	8	`int(11)`	range
`blockSizes`	96,376,113,87,93,78,183,201	`longblob`
`chromStarts`	0,165,592,707,847,1000,1155...	`longblob`
`id`	FBtr0073640	`varchar(255)`	values
`description`	FBgn0030367	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
CM001516	15218	16790	Cyp311a1-RB	490	+	15218	16790	8	96,376,113,87,93,78,183,201	0,165,592,707,847,1000,1155,1371	FBtr0073640	FBgn0030367
CM001516	17213	17984	CG14106-RA	388	+	17213	17984	3	75,69,117	0,156,654	FBtr0075858	FBgn0260459
CM001516	18565	20911	CG4281-RA	516	+	18570	20911	16	42,51,45,10,66,51,75,69,99,51,75,195,81,81,243,57	0,72,184,282,324,435,566,770,923,1216,1378,1453,1702,1849,1930,2289	FBtr0070339	FBgn0025626
CM001516	23729	30122	Sik2-RA	620	+	23729	29360	33	111,263,62,289,430,52,33,93,48,100,152,12,66,62,37,33,84,85,74,39,3,27,144,159,30,121,32,10,35,12,40,54,30	0,121,450,578,969,1634,1689,1908,2016,2072,2432,2698,2805,3033,3098,3135,3207,3348,3439,3624,3666,3678,3900,4182,4431,5510,5692, ...	FBtr0070340	FBgn0025625
CM001516	30092	31762	CG4313-RE	606	-	30602	31730	9	32,52,19,357,24,24,33,81,270	0,57,129,510,867,1022,1079,1172,1400	FBtr0340109	FBgn0025632
CM001516	30092	31765	CG4313-RC	604	-	30602	31730	9	32,52,19,357,24,24,33,81,273	0,57,129,510,867,1022,1079,1172,1400	FBtr0340107	FBgn0025632
CM001516	30092	32385	CG4313-RD	640	-	30602	32357	11	32,52,19,357,24,24,33,81,265,360,29	0,57,129,510,867,1022,1079,1172,1400,1734,2264	FBtr0340108	FBgn0025632
CM001516	40660	44370	moody-RB	660	+	42275	44350	11	27,15,140,523,282,49,95,61,129,69,57	0,247,1615,1844,2511,2796,2917,3212,3327,3522,3653	FBtr0303043	FBgn0025631
CM001516	40660	44370	moody-RD	660	+	42275	44250	11	27,15,140,523,282,49,93,61,129,69,57	0,247,1615,1844,2511,2796,2919,3212,3327,3522,3653	FBtr0303045	FBgn0025631
CM001516	41551	44370	moody-RA	656	+	42275	44350	10	36,140,523,282,49,95,61,129,69,57	0,724,953,1620,1905,2026,2321,2436,2631,2762	FBtr0070341	FBgn0025631

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

D. mel Transcripts (DmelTranscriptsBLAT) Track Description


	Description D. melanogaster transcripts annotated by FlyBase were aligned against the D. miranda genome assembly using a translated BLAT search. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions. Methods D. melanogaster transcripts were mapped against the D. miranda genome assembly using BLAT with the following parameters: `-q=rnax -t=dnax -mask=lower` The transcript alignments are analyzed by pslReps to identify the best alignments within the genome assembly that have a minimum alignment ratio of 0.25 (`-minAli=0.25`). The alignments are then filtered by pslCDnaFilter using the following parameters: -minId=0.35 -minCover=0.15 -localNearBest=0.010 -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Description

Methods

References