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

Database: DtakGB2 Primary Table: transposonPSIPfam Row Count: 2,388 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	AFFI02000003	`varchar(255)`	values
`chromStart`	2406	`int(10) unsigned`	range
`chromEnd`	3111	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	221	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	2406	`int(10) unsigned`	range
`thickEnd`	3111	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	705	`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
AFFI02000003	2406	3111	TPSI_PF00078_1	221	-	2406	3111	1	705	PF00078	RVT_1
AFFI02000004	1068	1368	TPSI_PF05380_2	216	-	1068	1368	1	300	PF05380	Peptidase_A17
AFFI02000004	20385	20985	TPSI_PF00078_3	200	+	20385	20985	1	600	PF00078	RVT_1
AFFI02000008	2890	3355	TPSI_PF05380_4	365	-	2890	3355	1	465	PF05380	Peptidase_A17
AFFI02000011	5083	5551	TPSI_PF05380_5	289	-	5083	5551	1	468	PF05380	Peptidase_A17
AFFI02000019	4563	4959	TPSI_PF00078_6	163	-	4563	4959	1	396	PF00078	RVT_1
AFFI02000022	807	1194	TPSI_PF00078_7	116	+	807	1194	1	387	PF00078	RVT_1
AFFI02000024	6645	7047	TPSI_PF00078_8	171	-	6645	7047	1	402	PF00078	RVT_1
AFFI02000024	11353	12094	TPSI_PF00078_9	239	-	11353	12094	1	741	PF00078	RVT_1
AFFI02000034	12600	12888	TPSI_PF00078_10	128	+	12600	12888	1	288	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