Schema for TransposonPSI (Pfam) - Pfam Transposon Protein Domains Identified by TransposonPSI
  Database: DbiaGB2    Primary Table: transposonPSIPfam    Row Count: 1,774   Data last updated: 2022-10-20
fieldexampleSQL type info
chrom AFFD02000013varchar(255) values
chromStart 2585int(10) unsigned range
chromEnd 2801int(10) unsigned range
name TPSI_PF14529_1varchar(255) values
score 141int(10) unsigned range
strand -char(1) values
thickStart 2585int(10) unsigned range
thickEnd 2801int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 1int(11) range
blockSizes 216longblob  
chromStarts 0longblob  
id PF14529varchar(255) values
description Exo_endo_phos_2longblob  

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsiddescription
AFFD0200001325852801TPSI_PF14529_1141-25852801012160PF14529Exo_endo_phos_2
AFFD0200002910301TPSI_PF01021_2360-10301012910PF01021TYA
AFFD020000374801083TPSI_PF00078_3143+4801083016030PF00078RVT_1
AFFD0200006081516TPSI_PF00078_4141-81516014350PF00078RVT_1
AFFD02000072605980TPSI_PF07253_5231-605980013750PF07253Gypsy
AFFD020000791289TPSI_PF07253_6171+1289012880PF07253Gypsy
AFFD0200008513461505TPSI_PF05380_7111+13461505011590PF05380Peptidase_A17
AFFD0200009422082481TPSI_PF00078_8124+22082481012730PF00078RVT_1
AFFD0200009896669TPSI_PF07253_9195-96669015730PF07253Gypsy
AFFD020001001751018122TPSI_PF07253_10169-1751018122016120PF07253Gypsy

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