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

Database: DyakCAF1 Primary Table: transposonPSIPfam Row Count: 2,450 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	616489	`int(10) unsigned`	range
`chromEnd`	617128	`int(10) unsigned`	range
`name`	TPSI_PF04094_1	`varchar(255)`	values
`score`	127	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	616489	`int(10) unsigned`	range
`thickEnd`	617128	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	639	`longblob`
`chromStarts`	0	`longblob`
`id`	PF04094	`varchar(255)`	values
`description`	DUF390	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
chr2L	616489	617128	TPSI_PF04094_1	127	+	616489	617128	1	639	PF04094	DUF390
chr2L	3740094	3740376	TPSI_PF00078_2	148	+	3740094	3740376	1	282	PF00078	RVT_1
chr2L	4173577	4174321	TPSI_PF00078_3	244	-	4173577	4174321	1	744	PF00078	RVT_1
chr2L	6527520	6527664	TPSI_PF11427_4	146	-	6527520	6527664	1	144	PF11427	HTH_Tnp_Tc3_1
chr2L	7403941	7404316	TPSI_PF00692_5	321	+	7403941	7404316	1	375	PF00692	dUTPase
chr2L	9637273	9637984	TPSI_PF00078_6	221	-	9637273	9637984	1	711	PF00078	RVT_1
chr2L	12245453	12246134	TPSI_PF00078_7	235	+	12245453	12246134	1	681	PF00078	RVT_1
chr2L	16476131	16476530	TPSI_PF00075_8	180	-	16476131	16476530	1	399	PF00075	RNase_H
chr2L	19414511	19415276	TPSI_PF00078_9	282	-	19414511	19415276	1	765	PF00078	RVT_1
chr2L	20558917	20559247	TPSI_PF05380_10	129	+	20558917	20559247	1	330	PF05380	Peptidase_A17

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