Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements.

ABSTRACT:

Background

Long interspersed nuclear elements (LINES) are the most common transposable element (TE) in almost all metazoan genomes examined. In most LINE superfamilies there are two open reading frames (ORFs), and both are required for transposition. The ORF2 is well characterized, while the structure and function of the ORF1 is less well understood. ORF1s have been classified into five types based on structural organization and the domains identified. Here we perform a large scale analysis of ORF1 domains of 448 elements from the Jockey superfamily using multiple alignments and Hidden Markov Model (HMM)-HMM comparisons.

Results

Three major lineages, Chicken repeat 1 (CR1), LINE2 (L2) and Jockey, were identified. All Jockey lineage elements have the same type of ORF1. In con

SUBMITTER: Metcalfe CJ 

PROVIDER: S-EPMC4120745 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature