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

Database: DeugGB2 Primary Table: transposonPSIPfam Row Count: 2,331 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	AFPQ02000031	`varchar(255)`	values
`chromStart`	34936	`int(10) unsigned`	range
`chromEnd`	35293	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	156	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	34936	`int(10) unsigned`	range
`thickEnd`	35293	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	357	`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	chromStarts	id	description
AFPQ02000031	34936	35293	TPSI_PF00078_1	156	-	34936	35293	1	357	0	PF00078	RVT_1
AFPQ02000070	0	489	TPSI_PF00078_2	219	+	0	489	1	489	0	PF00078	RVT_1
AFPQ02000070	625	1153	TPSI_PF00078_3	220	-	625	1153	1	528	0	PF00078	RVT_1
AFPQ02000151	1182	1947	TPSI_PF07253_4	198	-	1182	1947	1	765	0	PF07253	Gypsy
AFPQ02000162	16	514	TPSI_PF07253_5	305	-	16	514	1	498	0	PF07253	Gypsy
AFPQ02000182	2452	3351	TPSI_PF07253_6	236	-	2452	3351	2	285,549	0,350	PF07253	Gypsy
AFPQ02000231	6298	6982	TPSI_PF00078_7	180	-	6298	6982	1	684	0	PF00078	RVT_1
AFPQ02000231	15270	15402	TPSI_PF05380_8	156	+	15270	15402	1	132	0	PF05380	Peptidase_A17
AFPQ02000233	86	710	TPSI_PF07253_9	288	+	86	710	1	624	0	PF07253	Gypsy
AFPQ02000256	4219	4576	TPSI_PF07253_10	211	-	4219	4576	1	357	0	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