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

Database: DkikGB2 Primary Table: transposonPSIPfam Row Count: 2,225 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	AFFH02000021	`varchar(255)`	values
`chromStart`	34	`int(10) unsigned`	range
`chromEnd`	295	`int(10) unsigned`	range
`name`	TPSI_PF07253_1	`varchar(255)`	values
`score`	170	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	34	`int(10) unsigned`	range
`thickEnd`	295	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(11)`	range
`blockSizes`	261	`longblob`
`chromStarts`	0	`longblob`
`id`	PF07253	`varchar(255)`	values
`description`	Gypsy	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	id	description
AFFH02000021	34	295	TPSI_PF07253_1	170	-	34	295	1	261	0	PF07253	Gypsy
AFFH02000028	1092	1437	TPSI_PF00078_2	160	+	1092	1437	1	345	0	PF00078	RVT_1
AFFH02000051	815	1130	TPSI_PF05380_3	117	-	815	1130	1	315	0	PF05380	Peptidase_A17
AFFH02000071	25	445	TPSI_PF00078_4	158	-	25	445	1	420	0	PF00078	RVT_1
AFFH02000099	3	153	TPSI_PF14214_5	126	+	3	153	1	150	0	PF14214	Helitron_like_N
AFFH02000105	868	1390	TPSI_PF00078_6	193	-	868	1390	1	522	0	PF00078	RVT_1
AFFH02000113	1035	1488	TPSI_PF00078_7	230	-	1035	1488	1	453	0	PF00078	RVT_1
AFFH02000113	2134	2461	TPSI_PF14529_8	112	-	2134	2461	1	327	0	PF14529	Exo_endo_phos_2
AFFH02000140	545	1017	TPSI_PF05380_9	188	+	545	1017	2	102,369	0,103	PF05380	Peptidase_A17
AFFH02000140	6979	7315	TPSI_PF14529_10	112	+	6979	7315	1	336	0	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