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

Database: DperCAF1 Primary Table: transposonPSIPfam Row Count: 4,207 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	super_0	`varchar(255)`	values
`chromStart`	1072870	`int(10) unsigned`	range
`chromEnd`	1073218	`int(10) unsigned`	range
`name`	TPSI_PF14529_1	`varchar(255)`	values
`score`	162	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1072870	`int(10) unsigned`	range
`thickEnd`	1073218	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	348	`longblob`
`chromStarts`	0	`longblob`
`id`	PF14529	`varchar(255)`	values
`description`	Exo_endo_phos_2	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
super_0	1072870	1073218	TPSI_PF14529_1	162	+	1072870	1073218	1	348	PF14529	Exo_endo_phos_2
super_0	1074001	1074760	TPSI_PF00078_2	296	+	1074001	1074760	1	759	PF00078	RVT_1
super_0	3270498	3271140	TPSI_PF00078_3	233	+	3270498	3271140	1	642	PF00078	RVT_1
super_0	3292847	3293294	TPSI_PF00078_4	195	+	3292847	3293294	1	447	PF00078	RVT_1
super_0	3305312	3305675	TPSI_PF07727_5	198	-	3305312	3305675	1	363	PF07727	RVT_2
super_0	3307267	3307480	TPSI_PF00078_6	158	-	3307267	3307480	1	213	PF00078	RVT_1
super_0	3307877	3308072	TPSI_PF00078_7	135	-	3307877	3308072	1	195	PF00078	RVT_1
super_0	3314364	3314709	TPSI_PF00078_8	151	+	3314364	3314709	1	345	PF00078	RVT_1
super_0	3315383	3315728	TPSI_PF14529_9	143	+	3315383	3315728	1	345	PF14529	Exo_endo_phos_2
super_0	4373135	4373894	TPSI_PF00078_10	296	-	4373135	4373894	1	759	PF00078	RVT_1

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