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

Database: DserGB1 Primary Table: DmelTranscriptsBLAT Row Count: 33,166 Data last updated: 2024-01-05

field	example	SQL type	info
`chrom`	MTTC01000009	`varchar(255)`	values
`chromStart`	28638	`int(10) unsigned`	range
`chromEnd`	92302	`int(10) unsigned`	range
`name`	Wnt5-RB	`varchar(255)`	values
`score`	488	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	28638	`int(10) unsigned`	range
`thickEnd`	92302	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	8	`int(11)`	range
`blockSizes`	57,105,57,213,63,123,201,174	`longblob`
`chromStarts`	0,62154,62496,62571,63016,6...	`longblob`
`id`	FBtr0343046	`varchar(255)`	values
`description`	FBgn0010194	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
MTTC01000009	28638	92302	Wnt5-RB	488	-	28638	92302	8	57,105,57,213,63,123,201,174	0,62154,62496,62571,63016,63109,63289,63490	FBtr0343046	FBgn0010194
MTTC01000009	28638	92302	Wnt5-RA	488	-	28638	92302	8	57,105,57,213,63,123,201,174	0,62154,62496,62571,63016,63109,63289,63490	FBtr0074623	FBgn0010194
MTTC01000009	164697	177206	CG10417-RA	598	+	164697	177206	6	111,273,81,114,480,135	0,7097,7379,7514,8196,12374	FBtr0086091	FBgn0033021
MTTC01000009	164697	177206	CG10417-RB	598	+	164697	177206	6	111,273,81,114,480,135	0,7097,7379,7514,8196,12374	FBtr0086092	FBgn0033021
MTTC01000009	263516	263849	CG10395-RD	486	-	263516	263849	2	174,147	0,186	FBtr0347209	FBgn0033019
MTTC01000009	263516	263849	CG10395-RE	486	-	263516	263849	2	174,147	0,186	FBtr0347210	FBgn0033019
MTTC01000009	943659	944294	Tsp42Ef-RA	570	-	943659	944294	2	123,512	0,123	FBtr0089023	FBgn0033127
MTTC01000009	973719	974121	GlcAT-S-RA	392	-	973719	974121	4	132,11,99,129	0,133,174,273	FBtr0079841	FBgn0032135
MTTC01000009	973719	974195	GlcAT-S-RB	384	-	973719	974175	5	132,11,99,129,21	0,133,174,273,455	FBtr0079842	FBgn0032135
MTTC01000009	973719	974195	GlcAT-S-RC	378	-	973719	974175	5	132,11,99,129,21	0,133,174,273,455	FBtr0302199	FBgn0032135

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. serrata 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. serrata 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