title: RhesusBase: a knowledgebase for the monkey research community.
abstract: 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.
authors.affiliation: Institute of Molecular Medicine, Peking University, Beijing, China.
authors.forename: Shi-Jian
authors.initials: SJ
authors.lastname: Zhang
authors.forename: Chu-Jun
authors.initials: CJ
authors.lastname: Liu
authors.forename: Mingming
authors.initials: M
authors.lastname: Shi
authors.forename: Lei
authors.initials: L
authors.lastname: Kong
authors.forename: Jia-Yu
authors.initials: JY
authors.lastname: Chen
authors.forename: Wei-Zhen
authors.initials: WZ
authors.lastname: Zhou
authors.forename: Xiaotong
authors.initials: X
authors.lastname: Zhu
authors.forename: Peng
authors.initials: P
authors.lastname: Yu
authors.forename: Jue
authors.initials: J
authors.lastname: Wang
authors.forename: Xinzhuang
authors.initials: X
authors.lastname: Yang
authors.forename: Ning
authors.initials: N
authors.lastname: Hou
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ye
authors.forename: Rongli
authors.initials: R
authors.lastname: Zhang
authors.forename: Ruiping
authors.initials: R
authors.lastname: Xiao
authors.forename: Xiuqin
authors.initials: X
authors.lastname: Zhang
authors.forename: Chuan-Yun
authors.initials: CY
authors.lastname: Li
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics; D020407:Internet; D051188:Knowledge Bases; D008253:Macaca mulatta / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D012333:RNA, Messenger