Background: 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.Result: 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.Conclusions: 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.
Bibliographical noteFunding Information:
Funding for the publication fee comes from National Natural Science Foundation of China (grant number: 31070752). This article has been published as part of BMC Genomics Volume 14 Supplement 8, 2013: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenomics/supplements/14/S8.
We thank Prof. Lei Liu, Dr. Guangyong Zheng, Dr. Zhen Wang, Jie Wang, and Tiancheng Liu, for their helpful comments and suggestions. This work was supported by the National Key Basic Research Program of China, known as 973 Program (grant number: 2011CB910204, grant number: 2010CB529206, grant number: 2010CB912702), the Research Program of The Chinese Academy of Sciences (grant number: KSCX2-EW-R-04, grant number: KSCX2-YW-R-190, grant number: 2011KIP204) and National Natural Science Foundation of China (grant number: 31070752).
- Conserved Element
- Overlapping transcripts
- Sequence Origin of Pldi and Ak158810 loci
- Substitution rate