Repbase Reports

2009, Volume 9, Issue 1
January 31, 2009
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 54

CR1-YB2_Pass

CR1 Non-LTR Retrotransposon from Passeriformes.

Submitted:
08-Jan-2009
Accepted:
31-Jan-2009
Key Words:
CR1; Non-LTR Retrotransposon; Transposable Element; CR1-YB2_Pass; LINE
Source:
Passeriformes
Organism:
Passeriformes
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae
[1] Authors:
Smit,A.F.
Title:
CR1-YB2_Pass - CR1 Non-LTR Retrotransposon from Passeriformes.
Journal:
Repbase Reports 9(1), 54-54 (2009)
Abstract:
15-18%. gag 1-805 (incomplete), pol 790-3782. Interesting story: 1) The pol is very close to that of chicken CR1-Y (79-80% at DNA level), the gag is close to that of chicken CR1-X (78% at DNA level) (chicken X & Y are only ~65% similar at the DNA level). The junction is confirmed by many copies. This indicates a recombination in the chicken or the finch lineage. Remember that the chicken gag tree did not correspond to the pol tree, so a recombination in the chicken lineage would make sense. 2) There is a distinct frameshift in the pol (pos 2959-2969 in this consensus, around AA 745 in related pols). The consensus is very clear and the frameshift seems to break the RT region (make sure), so the retrovirus must have had a frameshifting mechanism. The frameshift is not in the closely (75-80%) related CR1-Ya_Pass consensus.
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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