@article{Rose:Stadler:Molec_evolu_the:2011,
author = {Rose, Dominic and Stadler, Peter F.},
title = {Molecular evolution of the non-coding eosinophil granule 
         ontogeny transcript},
journal = {Front Genet},
year = {2011},
doi = {10.3389/fgene.2011.00069},
volume = {2},
user = {dominic},
pmid = {22303364},
pages = {69},
number = {},
issn = {1664-8021},
abstract = {Eukaryotic genomes are pervasively transcribed. A large 
            fraction of the transcriptional output consists of long, 
            mRNA-like, non-protein-coding transcripts (mlncRNAs). The 
            evolutionary history of mlncRNAs is still largely uncharted 
            territory. In this contribution, we explore in detail the 
            evolutionary traces of the eosinophil granule ontogeny 
            transcript (EGOT), an experimentally confirmed 
            representative of an abundant class of totally intronic 
            non-coding transcripts (TINs). EGOT is located antisense to 
            an intron of the ITPR1 gene. We computationally identify 
            putative EGOT orthologs in the genomes of 32 different 
            amniotes, including orthologs from primates, rodents, 
            ungulates, carnivores, afrotherians, and xenarthrans, as 
            well as putative candidates from basal amniotes, such as 
            opossum or platypus. We investigate the EGOT gene phylogeny, 
            analyze patterns of sequence conservation, and the 
            evolutionary conservation of the EGOT gene structure. We 
            show that EGO-B, the spliced isoform, may be present 
            throughout the placental mammals, but most likely dates back 
            even further. We demonstrate here for the first time that 
            the whole EGOT locus is highly structured, containing 
            several evolutionary conserved, and thermodynamic stable 
            secondary structures. Our analyses allow us to postulate 
            novel functional roles of a hitherto poorly understood 
            region at the intron of EGO-B which is highly conserved at 
            the sequence level. The region contains a novel ITPR1 exon 
            and also conserved RNA secondary structures together with a 
            conserved TATA-like element, which putatively acts as a 
            promoter of an independent regulatory element.}
}