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

Database: DpseGB3 Primary Table: transposonPSIPfam Row Count: 1,167 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	3237530	`int(10) unsigned`	range
`chromEnd`	3239087	`int(10) unsigned`	range
`name`	TPSI_PF04094_1	`varchar(255)`	values
`score`	133	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	3237530	`int(10) unsigned`	range
`thickEnd`	3239087	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	1557	`longblob`
`chromStarts`	0	`longblob`
`id`	PF04094	`varchar(255)`	values
`description`	DUF390	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
CH379058	3237530	3239087	TPSI_PF04094_1	133	+	3237530	3239087	1	1557	PF04094	DUF390
CH379058	4218377	4218905	TPSI_PF00078_2	176	-	4218377	4218905	1	528	PF00078	RVT_1
CH379059	965711	966125	TPSI_PF00078_3	125	-	965711	966125	1	414	PF00078	RVT_1
CH379059	969276	969690	TPSI_PF00078_4	131	-	969276	969690	1	414	PF00078	RVT_1
CH379059	981733	982159	TPSI_PF00078_5	129	+	981733	982159	1	426	PF00078	RVT_1
CH379059	988079	988469	TPSI_PF05380_6	280	+	988079	988469	1	390	PF05380	Peptidase_A17
CH379059	993656	993902	TPSI_PF05380_7	121	+	993656	993902	1	246	PF05380	Peptidase_A17
CH379059	1016216	1016420	TPSI_PF05380_8	139	+	1016216	1016420	1	204	PF05380	Peptidase_A17
CH379059	1070646	1070985	TPSI_PF00078_9	123	-	1070646	1070985	1	339	PF00078	RVT_1
CH379059	1076565	1077165	TPSI_PF00078_10	125	+	1076565	1077165	1	600	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