Schema for Drosophila RefSeq Transcripts - BLAT Alignment of Drosophila RefSeq Transcripts

Database: dm6 Primary Table: RefSeqRNA_DpseRefSeq1 Row Count: 28,916 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8876	`int(10) unsigned`	range
`chromEnd`	9014	`int(10) unsigned`	range
`name`	XM_033376754	`varchar(255)`	values
`score`	422	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	9013	`int(10) unsigned`	range
`thickEnd`	9014	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	138,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	chr2L	8876	9014	XM_033376754	422	-	9013	9014	1	138,	0,
585	chr2L	11214	17136	XM_015180145	530	-	11214	17136	13	27,78,61,140,141,125,479,106,399,747,774,3,84,	0,51,248,569,865,1071,1235,2305,2468,2909,3720,5588,5838,
585	chr2L	11214	17136	XM_001357063	530	-	11214	17136	13	27,78,61,140,141,125,479,106,399,747,774,3,84,	0,51,248,569,865,1071,1235,2305,2468,2909,3720,5588,5838,
585	chr2L	11462	15708	XR_004469370	524	-	11462	11462	9	54,141,141,125,479,106,399,747,774,	0,320,617,823,987,2057,2220,2661,3472,
585	chr2L	11462	15708	XR_004469371	524	-	11462	11462	9	54,141,141,125,479,106,399,747,774,	0,320,617,823,987,2057,2220,2661,3472,
585	chr2L	22113	23219	XM_033379902	560	-	22113	23219	4	141,412,194,225,	0,162,629,881,
585	chr2L	22113	24965	XM_002132433	534	-	22113	24965	7	141,412,194,531,315,282,219,	0,162,629,881,1445,1815,2633,
585	chr2L	22994	24965	XM_033380511	532	-	22994	24965	4	531,315,282,219,	0,564,934,1752,
585	chr2L	25570	59253	XM_001357062	530	-	26544	58150	60	39,38,12,7,19,9,37,144,199,438,225,193,71,75,15,36,165,36,72,120,90,171,213,21,69,60,126,57,73,39,60,21,75,12,93,96,42,42,75,96, ...	0,593,638,659,683,710,804,974,1195,1482,2444,3162,4822,5020,5160,5281,5464,5629,5728,5830,5977,6157,6337,6625,6739,6901,7150,751 ...
585	chr2L	25570	59253	XM_033380504	554	-	26544	58150	42	39,38,12,7,19,9,37,144,199,438,229,193,71,75,15,36,165,36,72,120,90,171,213,21,69,60,126,57,73,39,60,21,75,12,29,193,237,307,3,9 ...	0,593,638,659,683,710,804,974,1195,1482,2840,3162,4822,5020,5160,5281,5464,5629,5728,5830,5977,6157,6337,6625,6739,6901,7150,751 ...

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

Drosophila RefSeq Transcripts (ncbiDrosRefSeq) Track Description

Description

Drosophila transcripts from the NCBI RefSeq database were aligned against the D. melanogaster dm6 assembly using BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions.

Methods

RefSeq transcripts were mapped against the D. melanogaster genome assembly using BLAT with the following parameters: -repeats=lower -q=rnax -t=dnax -mask=lower

The transcript alignments are analyzed by pslReps using the following parameter: -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.

The transcripts were obtained from the NCBI FTP site under the following RefSeq assembly accession numbers:

Species	Assembly Name	RefSeq Accession
Drosophila melanogaster	Release 6 plus ISO1 MT	GCF_000001215.4
Drosophila mauritiana	ASM438214v1	GCF_004382145.1
Drosophila sechellia	ASM438219v2	GCF_004382195.2
Drosophila simulans	Prin_Dsim_3.1	GCF_016746395.2
Drosophila yakuba	Prin_Dyak_Tai18E2_2.1	GCF_016746365.2
Drosophila santomea	Prin_Dsan_1.1	GCF_016746245.2
Drosophila teissieri	Prin_Dtei_1.1	GCF_016746235.2
Drosophila erecta	DereRS2	GCF_003286155.1
Drosophila ficusphila	ASM1815226v1	GCF_018152265.1
Drosophila suzukii	LBDM_Dsuz_2.1.pri	GCF_013340165.1
Drosophila subpulchrella	RU_Dsub_v1.1	GCF_014743375.2
Drosophila biarmipes	RU_DBia_V1.1	GCF_025231255.1
Drosophila takahashii	ASM1815269v1	GCF_018152695.1
Drosophila eugracilis	ASM1815383v1	GCF_018153835.1
Drosophila rhopaloa	ASM1815211v1	GCF_018152115.1
Drosophila elegans	ASM1815250v1	GCF_018152505.1
Drosophila gunungcola	Dgunungcola_SK_2	GCF_025200985.1
Drosophila kikkawai	ASM1815253v1	GCF_018152535.1
Drosophila serrata	Dser1.0	GCF_002093755.1
Drosophila bipectinata	ASM1815384v1	GCF_018153845.1
Drosophila ananassae	ASM1763931v2	GCF_017639315.1
Drosophila pseudoobscura	UCI_Dpse_MV25	GCF_009870125.1
Drosophila persimilis	DperRS2	GCF_003286085.1
Drosophila miranda	D.miranda_PacBio2.1	GCF_003369915.1
Drosophila guanche	DGUA_6	GCF_900245975.1
Drosophila subobscura	UCBerk_Dsub_1.0	GCF_008121235.1
Drosophila obscura	ASM1815110v1	GCF_018151105.1
Drosophila willistoni	UCI_dwil_1.1	GCF_018902025.1
Drosophila arizonae	ASM165402v1	GCF_001654025.1
Drosophila mojavensis	ASM1815372v1	GCF_018153725.1
Drosophila navojoa	UFRJ_Dnav_4.2	GCF_001654015.2
Drosophila hydei	DhydRS2	GCF_003285905.1
Drosophila virilis	DvirRS2	GCF_003285735.1
Drosophila novamexicana	DnovRS2.1	GCF_003285875.2
Drosophila albomicans	ASM965048v2	GCF_009650485.2
Drosophila grimshawi	ASM1815329v1	GCF_018153295.1
Drosophila busckii	ASM1175060v1	GCF_011750605.1