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

Database: DbusGB1 Primary Table: transposonPSIPfam Row Count: 364 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	CP012523	`varchar(255)`	values
`chromStart`	4124438	`int(10) unsigned`	range
`chromEnd`	4125332	`int(10) unsigned`	range
`name`	TPSI_PF07253_1	`varchar(255)`	values
`score`	146	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	4124438	`int(10) unsigned`	range
`thickEnd`	4125332	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	894	`longblob`
`chromStarts`	0	`longblob`
`id`	PF07253	`varchar(255)`	values
`description`	Gypsy	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
CP012523	4124438	4125332	TPSI_PF07253_1	146	-	4124438	4125332	1	894	PF07253	Gypsy
CP012523	5099230	5099575	TPSI_PF00078_2	140	+	5099230	5099575	1	345	PF00078	RVT_1
CP012523	5249835	5250435	TPSI_PF00078_3	122	-	5249835	5250435	1	600	PF00078	RVT_1
CP012523	5254094	5254460	TPSI_PF07253_4	218	-	5254094	5254460	1	366	PF07253	Gypsy
CP012523	5285043	5285772	TPSI_PF00078_5	307	-	5285043	5285772	1	729	PF00078	RVT_1
CP012523	5286580	5286925	TPSI_PF14529_6	132	-	5286580	5286925	1	345	PF14529	Exo_endo_phos_2
CP012523	5305421	5305934	TPSI_PF00078_7	158	-	5305421	5305934	1	513	PF00078	RVT_1
CP012523	5348463	5349207	TPSI_PF00078_8	260	-	5348463	5349207	1	744	PF00078	RVT_1
CP012523	5365650	5365869	TPSI_PF05380_9	108	-	5365650	5365869	1	219	PF05380	Peptidase_A17
CP012523	5370523	5370778	TPSI_PF07253_10	172	+	5370523	5370778	1	255	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