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

Database: DereCAF1 Primary Table: transposonPSIPfam Row Count: 1,652 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	scaffold_1008	`varchar(255)`	values
`chromStart`	567	`int(10) unsigned`	range
`chromEnd`	1317	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	267	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	567	`int(10) unsigned`	range
`thickEnd`	1317	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	750	`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
scaffold_1008	567	1317	TPSI_PF00078_1	267	+	567	1317	1	750	PF00078	RVT_1
scaffold_1009	256	523	TPSI_PF00078_2	144	-	256	523	1	267	PF00078	RVT_1
scaffold_1010	97	703	TPSI_PF00078_3	169	+	97	703	1	606	PF00078	RVT_1
scaffold_1037	146	896	TPSI_PF00078_4	267	+	146	896	1	750	PF00078	RVT_1
scaffold_1115	2209	2410	TPSI_PF05380_5	163	+	2209	2410	1	201	PF05380	Peptidase_A17
scaffold_1116	655	1387	TPSI_PF00078_6	272	+	655	1387	1	732	PF00078	RVT_1
scaffold_1189	24	189	TPSI_PF00078_7	127	-	24	189	1	165	PF00078	RVT_1
scaffold_1198	271	700	TPSI_PF00078_8	130	-	271	700	1	429	PF00078	RVT_1
scaffold_1206	183	870	TPSI_PF00078_9	201	-	183	870	1	687	PF00078	RVT_1
scaffold_1206	1345	1678	TPSI_PF14529_10	131	-	1345	1678	1	333	PF14529	Exo_endo_phos_2

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