@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},
  volume =	 {2},
  number =	 {},
  pages =	 {69},
  user =	 {dominic},
  pmid =	 {22303364},
  doi = 	 {10.3389/fgene.2011.00069},
  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.}
}