Repbase Reports
2006, Volume 6, Issue 3
March 31, 2006
Copyright © 2001-2024 - Genetic Information Research Institute, California
ISSN# 1534-830X
Page 123

Gypsy-4-I_AF

Internal portion of the Gypsy-4_AF LTR retrotransposon.

Submitted:
03-Mar-2006 		Accepted:
12-APR-2006
Key Words:
Gypsy; LTR Retrotransposon; Transposable Element; Interspersed repeat; Gypsy superfamily; Gypsy-4_AF; Gypsy-4-LTR_AF; Gypsy-4-I_AF
Source:
Aspergillus fumigatus 		Organism:
Aspergillus fumigatus 		Taxonomy:
Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Aspergillaceae; Aspergillus
[] 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. et al.
    Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.
    Nature 438(7071), 1105-1115 (2005)

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