Schema for TransposonPSI (Pfam) - Pfam Transposon Protein Domains Identified by TransposonPSI

Database: DsecCAF1 Primary Table: transposonPSIPfam Row Count: 3,354 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	super_0	`varchar(255)`	values
`chromStart`	2708085	`int(10) unsigned`	range
`chromEnd`	2708703	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	179	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	2708085	`int(10) unsigned`	range
`thickEnd`	2708703	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	618	`longblob`
`chromStarts`	0	`longblob`
`id`	PF00078	`varchar(255)`	values
`description`	RVT_1	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
super_0	2708085	2708703	TPSI_PF00078_1	179	-	2708085	2708703	1	618	PF00078	RVT_1
super_0	2717982	2718576	TPSI_PF00078_2	176	+	2717982	2718576	1	594	PF00078	RVT_1
super_0	2826920	2827115	TPSI_PF05699_3	112	-	2826920	2827115	1	195	PF05699	Dimer_Tnp_hAT
super_0	3244445	3245189	TPSI_PF00078_4	244	-	3244445	3245189	1	744	PF00078	RVT_1
super_0	4715998	4716742	TPSI_PF00078_5	249	+	4715998	4716742	1	744	PF00078	RVT_1
super_0	5234938	5235682	TPSI_PF00078_6	247	-	5234938	5235682	1	744	PF00078	RVT_1
super_0	5236516	5236855	TPSI_PF14529_7	106	-	5236516	5236855	1	339	PF14529	Exo_endo_phos_2
super_0	7570524	7571268	TPSI_PF00078_8	251	+	7570524	7571268	1	744	PF00078	RVT_1
super_0	7646877	7647621	TPSI_PF00078_9	251	-	7646877	7647621	1	744	PF00078	RVT_1
super_0	8639565	8640945	TPSI_PF07253_10	755	+	8639565	8640945	1	1380	PF07253	Gypsy

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

TransposonPSI (Pfam) (transposonPSIPfam) Track Description


	Description This track shows the regions within the genome assembly that have sequence similarity to transposon protein domains in the Pfam database as identified by TransposonPSI. Methods A list of 124 transposon protein domains in the Pfam database have previously identified by Piriyapongsa and colleagues. Additional transposon protein domains in version 30.0 of the Pfam database were identified via text searches using the following keywords: DNA transposon, gag transposon, helitron, retroelements, retrotransposon, reverse transcriptase, transposon. References Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK. Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct. 2007 Nov 26;2:31. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. Brian J. Haas, TransposonPSI, 2007-2011 http://transposonpsi.sourceforge.net

Description