Repbase Reports

2010, Volume 10, Issue 1
January 31, 2010
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 103

Ambal-1_FCy

Ambal-1_FCy is a family of Ambal non-LTR retrotransposon - consensus.

Submitted:
26-Jan-2010
Accepted:
31-Jan-2010
Key Words:
Ambal; Non-LTR Retrotransposon; Transposable Element; Ambal-1_FCy
Source:
Fragilariopsis cylindrus
Organism:
Fragilariopsis cylindrus
Taxonomy:
Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Ambal, a novel clade of non-LTR retrotransposons from diatoms.
Journal:
Repbase Reports 10(1), 103-103 (2010)
Abstract:
Ambal is a novel clade of gigantic non-LTR retrotransposons identified in the Fragilariopsis cylindrus and Thalassiosira pseudonana diatom genomes. Typical Ambal is about 10-13 kb long and codes for two ORFs. While classification and function of the ORF1 protein are not clear, the ORF2 protein contains three conserved domains: apurinic endonuclease, reverse transcriptase and riboniuclease H domains. Usually, 5' termini of Ambals are composed of family-specific microsatellites. Ambals are flanked by target site dupliations (from 7 to 20-bp). The ~100-bp long 5' terminal portion is conserved in diverse families of Ambals (e.g. Ambal-1_FCy and Ambal-2_FCy, Ambal-2_FCy and Ambal-3_FCy). Most likely it contains the pol II internal promoter necessary for retrotransposition of Ambals. The diatome genomes contain also families of short non-autonomous Ambals that share with autonomous Ambals both the 5' and 3' terminal portions (analogously to Ingi non-LTR retrotransposons), e.g. Ambal-3N1_FCy and Ambal-1N1_TP. The Ambal-1_FCy consensus sequence was derived from 3 copies >99% identical to each other. Ambal-1_FCy is characterized by ~15-bp TSDs. This family can be still active. The consensus sequence was derived from sequence data produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community.
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

© 2001-2019 - Genetic Information Research Institute