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

Database: DanaCAF1 Primary Table: transposonPSIPfam Row Count: 7,238 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	scaffold_10002	`varchar(255)`	values
`chromStart`	6107	`int(10) unsigned`	range
`chromEnd`	6770	`int(10) unsigned`	range
`name`	TPSI_PF00078_1	`varchar(255)`	values
`score`	218	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	6107	`int(10) unsigned`	range
`thickEnd`	6770	`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
scaffold_10002	6107	6770	TPSI_PF00078_1	218	-	6107	6770	1	663	PF00078	RVT_1
scaffold_10006	1576	2062	TPSI_PF05380_2	303	-	1576	2062	1	486	PF05380	Peptidase_A17
scaffold_10010	1403	1883	TPSI_PF05380_3	379	+	1403	1883	1	480	PF05380	Peptidase_A17
scaffold_10011	3784	4123	TPSI_PF14529_4	150	+	3784	4123	1	339	PF14529	Exo_endo_phos_2
scaffold_10011	4912	5683	TPSI_PF00078_5	271	+	4912	5683	1	771	PF00078	RVT_1
scaffold_10011	10305	10917	TPSI_PF00078_6	213	+	10305	10917	1	612	PF00078	RVT_1
scaffold_10015	4584	4818	TPSI_PF05380_7	136	+	4584	4818	1	234	PF05380	Peptidase_A17
scaffold_10022	1016	1238	TPSI_PF05380_8	125	-	1016	1238	1	222	PF05380	Peptidase_A17
scaffold_10026	3030	3531	TPSI_PF00078_9	154	+	3030	3531	1	501	PF00078	RVT_1
scaffold_10029	7	661	TPSI_PF00078_10	203	+	7	661	1	654	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