Repbase Reports |
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| 2010, Volume 10, Issue 1 |
| January 31, 2010 |
| Copyright © 2001-2024 - Genetic Information Research Institute, California |
| ISSN# 1534-830X |
| Page 103 |
Ambal-1_FCy |
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Ambal-1_FCy is a family of Ambal non-LTR retrotransposon - consensus. |
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Submitted: 26-Jan-2010 |
Accepted: 26-JAN-2010 |
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Key Words: Ambal; Non-LTR Retrotransposon; Transposable Element; Ambal-1_FCy |
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Source: Fragilariopsis cylindrus |
Organism: Fragilariopsis cylindrus |
Taxonomy: Eukaryota; Stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis |
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Authors: Kapitonov,V.V. and Jurka,J. |
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Title: Ambal, a novel clade of non-LTR retrotransposons from diatoms. |
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Journal: Repbase Reports 10(1), 103-103 (2010) |
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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.
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Derived: [1] (Consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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