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

Database: DhydGB1 Primary Table: transposonPSIPfam Row Count: 245 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	NWQH01000001	`varchar(255)`	values
`chromStart`	13254	`int(10) unsigned`	range
`chromEnd`	14394	`int(10) unsigned`	range
`name`	TPSI_PF07253_1	`varchar(255)`	values
`score`	679	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	13254	`int(10) unsigned`	range
`thickEnd`	14394	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	1140	`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
NWQH01000001	13254	14394	TPSI_PF07253_1	679	+	13254	14394	1	1140	PF07253	Gypsy
NWQH01000001	16192	16555	TPSI_PF07253_2	205	+	16192	16555	1	363	PF07253	Gypsy
NWQH01000002	2642459	2642855	TPSI_PF00078_3	127	-	2642459	2642855	1	396	PF00078	RVT_1
NWQH01000007	1131777	1131987	TPSI_PF01498_4	110	-	1131777	1131987	1	210	PF01498	HTH_Tnp_Tc3_2
NWQH01000008	0	873	TPSI_PF07253_5	514	+	0	873	1	873	PF07253	Gypsy
NWQH01000012	992267	992399	TPSI_PF00429_6	122	-	992267	992399	1	132	PF00429	TLV_coat
NWQH01000013	19379	20030	TPSI_PF07253_7	281	-	19379	20030	1	651	PF07253	Gypsy
NWQH01000015	945	2034	TPSI_PF07253_8	407	+	945	2034	1	1089	PF07253	Gypsy
NWQH01000015	16616	16913	TPSI_PF07253_9	136	+	16616	16913	1	297	PF07253	Gypsy
NWQH01000015	573159	573579	TPSI_PF07253_10	151	-	573159	573579	1	420	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