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

Database: DobsGB1 Primary Table: transposonPSIPfam Row Count: 2,287 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	BDQP01000001	`varchar(255)`	values
`chromStart`	529987	`int(10) unsigned`	range
`chromEnd`	530650	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	266	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	529987	`int(10) unsigned`	range
`thickEnd`	530650	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	663	`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
BDQP01000001	529987	530650	TPSI_PF00078_1	266	-	529987	530650	1	663	PF00078	RVT_1
BDQP01000002	589430	590234	TPSI_PF04094_2	123	+	589430	590234	1	804	PF04094	DUF390
BDQP01000002	1023473	1023779	TPSI_PF05380_3	260	-	1023473	1023779	1	306	PF05380	Peptidase_A17
BDQP01000003	10927	11629	TPSI_PF00078_4	275	+	10927	11629	1	702	PF00078	RVT_1
BDQP01000003	16198	16450	TPSI_PF05380_5	155	-	16198	16450	1	252	PF05380	Peptidase_A17
BDQP01000003	16448	16673	TPSI_PF05380_6	171	-	16448	16673	1	225	PF05380	Peptidase_A17
BDQP01000003	23975	24461	TPSI_PF05380_7	314	+	23975	24461	1	486	PF05380	Peptidase_A17
BDQP01000003	27196	27472	TPSI_PF00078_8	119	+	27196	27472	1	276	PF00078	RVT_1
BDQP01000003	31771	32431	TPSI_PF00078_9	253	+	31771	32431	1	660	PF00078	RVT_1
BDQP01000003	37427	37739	TPSI_PF14529_10	127	+	37427	37739	1	312	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