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Zhou, Q., Zhang, G., Zhang, Y., Xu, S., Zhao, R., Zhan, Z., Li, X., Ding, Y., Yang, S. and Wang, W. (2008) On the origin of new genes in Drosophila. Genome Research, 18, 1446-1455. doi:10.1101/gr.076588.108

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• TITLE: Evolutionarily conserved features of the retained intron in alternative transcripts of the nxf1 (nuclear export factor) genes in different organisms

  AUTHORS: Ludmila A. Mamon, Sergey F. Kliver, Elena V. Golubkova

  KEYWORDS: Nxf; Intron Retention; CTE; Poly(A); Drosophila; Vertebrates

  JOURNAL NAME: Open Journal of Genetics, Vol.3 No.3, August 28, 2013

  ABSTRACT: One of the features of intron-containing genes of the nxf (nuclear export factor) family in different organisms is the presence of an evolutionarily conserved exon-intron block: exon 110nt-intron-exon 37nt. The intron in this evolutionarily conserved block, which we call a “cassette” intron, can be excised or retained in alternative transcripts of nxf1. It corresponds to intron 10 -11 inthe genes that are orthologous to nxf1 in vertebrates, and intron 5 -6 inthe genes that are orthologous to nxf1 in Drosophilidae. The alignment of sequences of cassette introns in nxf1 genes in vertebrates has revealed four evolutionarily conserved sequences: 1)5’flanking sequence, 2) a region containing СТЕ (constitutive transport element), 3) third conserved sequence, and 4)3’flanking sequence. Introns 5-6 of nxf1 in Drosophilidae have no similar conserved sequences. The results of sequence alignment demonstrate a similarity between cassette introns of nxf1 in Drosophilidae in two poly(A) sequences. The prevalence of Dm nxf1 transcripts containing cassette intron 5-6 under completely spliced transcripts in the heads of adult Drosophila melanogaster suggests a functional importance of transcripts that contain a retained intron. Evolutionary conservation, which in Drosophilidae is evident in the presence of poly(A) sequences in cassette introns of the nxf1 genes, is an adaptive feature: the poly(A) sequences are capable of mimicking the 3’-end of transcripts, promote transport from the nucleus to the cytoplasm, or are involved in NMD control. The ability to form characteristic secondary structures is a common feature of nxf1 cassette introns.