Repbase Reports
2006, Volume 6, Issue 3
March 31, 2006
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 123

Gypsy-4-I_AF

Internal portion of the Gypsy-4_AF LTR retrotransposon.

Submitted:
03-Mar-2006 		Accepted:
31-Mar-2006
Key Words:
Gypsy; LTR Retrotransposon; Interspersed Repeat; Gypsy superfamily; Gypsy-4_AF; Gypsy-4-LTR_AF; Gypsy-4-I_AF
Source:
Aspergillus fumigatus 		Organism:
Aspergillus fumigatus 		Taxonomy:
Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
[2] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy-4_AF, a family of gypsy LTR retrotransposons in the Aspergillus fumigatus genome.
Journal:
Repbase Reports 6(3), 123-123 (2006)
Abstract:
This is an internal portion of the Gypsy-4_AF LTR retrotransposon. One copy of Gypsy-4-I_AF is flanked by identical LTRs (contig 1.12). Its internal sequence, reported here, encodes a well preserved polyprotein composed of reverse transcriptase, endonuclease and chromodomain (only a few stop codons). There are 4 other copies of Gypsy-4-I_AF present in the genome that are 77-84% identical to Gypsy-4-I_AF. Their ORFs encoding the corresponding polyproteins are severely damaged by many stop-codons due to transitions. The transition/transversion ratio is amazingly high, most likely because of RIP (quick mutations of CpG to CpA and TpG, CpA to TpA, and TpG to TpA). For example, Gypsy-4-I_AF and its cosmid1.16 copy are 77% identical. Among the corresponding 1582 mismatches, 1575 are transitions (only 2 gaps). The corresponding transition/transversion ratio is 225!.
Derived:
[2] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Galagan,J.E., Calvo,S.E., Cuomo,C., Ma,L.J., Wortman,J.R., Batzoglou,S., Lee,S.I., Spevak,C.C., Basturkmen,M., Clutterbuck,J., Kapitonov,V., Jurka,J., Scazzocchio,C., Farman,M., Butler,J., Purcell,S., Harris,S., Braus,G.H., Draht,O., Busch,S., D'Enfert,C., Bouchier,C., Goldman,G.H., Bell-Pedersen,D., Griffiths-Jones,S., Doonan,J.H., Yu,J., Vienken,K., Pain,A., Freitag,M., Selker,E.U., Archer,D.B., Penalva,M.A., Oakley,B.R., Momany,M., Tanaka,T., Kumagai,T., Asai,K., Machida,M., Nierman,W.C., Denning,D.W., Caddick,M., Hynes,M., Paoletti,M., Fischer,R., Miller,B., Dyer,P., Sachs,M.S., Osmani,S.A. and Birren,B.W.
    Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.
    Nature 438(7071), 1105-1115 (2005)

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