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

Database: DpseGB3 Primary Table: DmelTranscriptsBLAT Row Count: 30,461 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	17129	`int(10) unsigned`	range
`chromEnd`	22388	`int(10) unsigned`	range
`name`	CG13991-RA	`varchar(255)`	values
`score`	556	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	17129	`int(10) unsigned`	range
`thickEnd`	22388	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	8	`int(11)`	range
`blockSizes`	273,51,768,1558,33,126,1575...	`longblob`
`chromStarts`	0,282,363,1211,3177,3270,34...	`longblob`
`id`	FBtr0079202	`varchar(255)`	values
`description`	FBgn0031785	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
CH379058	17129	22388	CG13991-RA	556	-	17129	22388	8	273,51,768,1558,33,126,1575,180	0,282,363,1211,3177,3270,3423,5079	FBtr0079202	FBgn0031785
CH379058	27063	27174	CG33927-RA	364	-	27063	27174	1	111	0	FBtr0091931	FBgn0053927
CH379058	57378	58461	CG9222-RA	636	+	57378	58461	7	81,271,316,65,78,45,48	0,122,458,836,906,987,1035	FBtr0079201	FBgn0031784
CH379058	58802	61378	B9d2-RA	448	+	58810	59477	9	97,354,125,45,277,228,294,282,234	0,170,583,734,1064,1400,1700,2024,2342	FBtr0303078	FBgn0261683
CH379058	58802	61378	tctn-RA	448	+	59478	61378	9	97,354,125,45,277,228,294,282,234	0,170,583,734,1064,1400,1700,2024,2342	FBtr0303079	FBgn0261697
CH379058	61562	64679	sac-RB	552	-	61562	64679	1	3117	0	FBtr0299947	FBgn0037254
CH379058	68609	70362	WDR79-RB	498	+	68609	70362	6	18,57,303,390,300,45	0,54,564,922,1324,1708	FBtr0333407	FBgn0031782
CH379058	68609	70362	WDR79-RC	498	+	68609	70362	6	18,57,303,390,300,45	0,54,564,922,1324,1708	FBtr0346267	FBgn0031782
CH379058	70425	71056	Arpc4-RA	784	-	70546	71054	2	34,512	0,119	FBtr0079200	FBgn0284255
CH379058	72539	115508	stai-RB	738	-	74330	115478	12	36,27,18,10,21,81,162,141,186,170,73,110	0,417,663,692,1557,1791,2014,2842,3045,3320,31784,42859	FBtr0079197	FBgn0266521

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. pseudoobscura 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. pseudoobscura 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