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This article is part of the supplement: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Genomics

Open Access Research

The de novo sequence origin of two long non-coding genes from an inter-genic region

Yulin Dai12, Shengdi Li12, Xiao Dong12, Han Sun123, Chao Li12, Zhi Liu12, Beili Ying4, Guohui Ding13* and Yixue Li13*

Author Affiliations

1 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd. Shanghai 200031, PR China

2 Graduate School of Chinese Academy of Sciences, 19 Yuquan Rd. Beijing 100049, PR China

3 Shanghai Center for Bioinformation Technology, 1278 Keyuan Rd. Shanghai 201203, PR China

4 School of Life Sciences, Fudan University, 220 Handan Rd. Shanghai 200433, PR China

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BMC Genomics 2013, 14(Suppl 8):S6  doi:10.1186/1471-2164-14-S8-S6

Published: 9 December 2013



The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can only be expressed in mouse testis with a mouse-specific transcription start site. The consensus sequence of Pldi is also part of an antisense transcript AK158810 expressed in a wide range of mouse tissues.


We focused on sequence origin of Pldi and Ak158810. We demonstrated that their sequence was originated from an inter-genic region and is only presented in mammalians. Transposable events and chromosome rearrangements were involved in the evolution of ancestral sequence. Moreover, we discovered high conservation in part of this region was correlated with chromosome rearrangements, CpG demethylation and transcriptional factor binding motif. These results demonstrated that multiple factors contributed to the sequence origin of Pldi.


We comprehensively analyzed the sequence origin of Pldi-Ak158810 loci. We provided various factors, including rearrangement, transposable elements, contributed to the formation of the sequence.

Overlapping transcripts; Sequence Origin of Pldi and Ak158810 loci; Conserved Element; Substitution rate