RhesusBase Edit

Citations: 18

z-index: 3.6

Basic information
Short name RhesusBase
Full name
Description RhesusBase was thus developed to refine genome-wide macaque gene structures, to integrate macaque functional annotations, and to provide a 'one-stop' knowledgebase for the primate research community
URL http://www.rhesusbase.org/
Year founded 2012
Last update & version 2013-04-01 v2.0
Availability Free to all users
Contact information
University/Institution hosted Peking University
Address Institute of Molecular Medicine,Peking University,Beijing,China
City Beijing
Province/State
Country/Region China
Contact name Chuan-Yun Li
Contact email chuanyunli@pku.edu.cn
Data information
Object(s)
Data type(s)
  • DNA
Data Category/Categories
  • Structure
Major organism(s)
  • Macaca mulatta
Keyword(s)
  • gene structure
  • NGS datasets
Publications
  • RhesusBase: a knowledgebase for the monkey research community.[PMID: 22965133]
    Shi-Jian Zhang, Chu-Jun Liu, Mingming Shi, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuang Yang, Ning Hou, Zhiqiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang, Chuan-Yun Li

    Although the rhesus macaque is a unique model for the translational study of human diseases, currently its use in biomedical research is still in its infant stage due to error-prone gene structures and limited annotations. Here, we present RhesusBase for the monkey research community (http://www.rhesusbase.org). We performed strand-specific RNA-Seq studies in 10 macaque tissues and generated 1.2 billion 90-bp paired-end reads, covering >97.4% of the putative exon in macaque transcripts annotated by Ensembl. We found that at least 28.7% of the macaque transcripts were previously mis-annotated, mainly due to incorrect exon-intron boundaries, incomplete untranslated regions (UTRs) and missed exons. Compared with the previous gene models, the revised transcripts show clearer sequence motifs near splicing junctions and the end of UTRs, as well as cleaner patterns of exon-intron distribution for expression tags and cross-species conservation scores. Strikingly, 1292 exon-intron boundary revisions between coding exons corrected the previously mis-annotated open reading frames. The revised gene models were experimentally verified in randomly selected cases. We further integrated functional genomics annotations from >60 categories of public and in-house resources and developed an online accessible database. User-friendly interfaces were developed to update, retrieve, visualize and download the RhesusBase meta-data, providing a 'one-stop' resource for the monkey research community.

    Nucleic acids research 2013:41(Database issue)

    18 Citations (from Europe PMC, 2018-10-12)

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Record metadata

  • Created on: 2015-06-21
    • Xia Lin [2016-04-01]
    • Xia Lin [2015-11-23]
    • Xia Lin [2015-06-26]

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