Science China Life Sciences

, Volume 60, Issue 2, pp 178–188 | Cite as

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

Open Access
Research Paper


Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development.


ortholog alternative splicing RNA-seq early embryo gene expression 



We would like to thank Li Zhang and Rong Cheng from East China Normal University for their helpful discussions. We are also grateful to the Supercomputer Center of East China Normal University. This work was supported by the China Human Proteomics Project (2014DFB30010), the National High Technology Research and Development Program of China (2015AA020104,), the National Natural Science Foundation of China (31071162), and the Graduate School of East China Normal University.

Supplementary material

11427_2015_348_MOESM1_ESM.doc (296 kb)
Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos
11427_2015_348_MOESM2_ESM.xls (68 kb)
Extreme examples where human genes hold large number of isoforms (>=20) compare to mouse (<=5).
11427_2015_348_MOESM3_ESM.xls (42 kb)
Human and mouse orthologous splicing regulators.


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Copyright information

© The Author(s) 2016

Authors and Affiliations

  • Geng Chen
    • 1
    • 2
  • Jiwei Chen
    • 1
  • Jianmin Yang
    • 1
  • Long Chen
    • 1
  • Xiongfei Qu
    • 1
  • Caiping Shi
    • 1
  • Baitang Ning
    • 3
  • Leming Shi
    • 2
    • 3
  • Weida Tong
    • 3
  • Yongxiang Zhao
    • 4
  • Meixia Zhang
    • 5
  • Tieliu Shi
    • 1
  1. 1.The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghaiChina
  2. 2.Center for Pharmacogenomics, School of PharmacyFudan UniversityShanghaiChina
  3. 3.National Center for Toxicological ResearchUS Food and Drug AdministrationJeffersonUSA
  4. 4.Biological Targeting Diagnosis and Therapy Research CenterGuangxi Medical UniversityNanningChina
  5. 5.Department of Ophthalmology, West China HospitalSichuan UniversityChengduChina

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