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The Xenopus ORFeome: a resource that enables functional genomics
journal contributionposted on 2020-07-28, 13:32 authored by Ian M Grant, Dawit Balcha, Tong Hao, Yun Shen, Prasad Trivedi, Ilya Patrushev, Joshua D Fortriede, John B Karpinka, Limin Liu, Aaron M Zorn, P Todd Stukenberg, David E Hill, Michael J Gilchrist
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
GatewayGene annotationORFeomeOpen reading frameRecombinational cloningXenopusAnimalsBase SequenceCloning, MolecularDNA, ComplementaryDatabases, GeneticDiseaseGenomicsHumansModels, GeneticMolecular Sequence DataOpen Reading FramesSequence Homology, Nucleic AcidSpecies SpecificityXenopus ProteinsXenopus laevisGilchrist U117597137Developmental Biology06 Biological Sciences11 Medical and Health Sciences