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

Database: DmirGB2 Primary Table: transposonPSIPfam Row Count: 417 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	175619	`int(10) unsigned`	range
`chromEnd`	175952	`int(10) unsigned`	range
`name`	TPSI_PF14529_1	`varchar(255)`	values
`score`	129	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	175619	`int(10) unsigned`	range
`thickEnd`	175952	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	333	`longblob`
`chromStarts`	0	`longblob`
`id`	PF14529	`varchar(255)`	values
`description`	Exo_endo_phos_2	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	id	description
CM001516	175619	175952	TPSI_PF14529_1	129	+	175619	175952	1	333	PF14529	Exo_endo_phos_2
CM001516	815788	816046	TPSI_PF00078_2	168	+	815788	816046	1	258	PF00078	RVT_1
CM001516	1039554	1039908	TPSI_PF05380_3	238	-	1039554	1039908	1	354	PF05380	Peptidase_A17
CM001516	1070631	1071096	TPSI_PF05380_4	287	+	1070631	1071096	1	465	PF05380	Peptidase_A17
CM001516	1126397	1126721	TPSI_PF07253_5	141	+	1126397	1126721	1	324	PF07253	Gypsy
CM001516	1142838	1143561	TPSI_PF00078_6	220	-	1142838	1143561	1	723	PF00078	RVT_1
CM001516	1279794	1279977	TPSI_PF01498_7	110	-	1279794	1279977	1	183	PF01498	HTH_Tnp_Tc3_2
CM001516	1393010	1393190	TPSI_PF01498_8	101	-	1393010	1393190	1	180	PF01498	HTH_Tnp_Tc3_2
CM001516	1446261	1446495	TPSI_PF00078_9	114	+	1446261	1446495	1	234	PF00078	RVT_1
CM001516	1451615	1452290	TPSI_PF00078_10	160	+	1451615	1452290	1	675	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