2024•International Journal of Molecular SciencesOpen access
SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms
Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele C. Neves‐Ferreira, Paulo C. Carvalho, Flávia Cristina de Paula Freitas, Fábio Passetti
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Abstract
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.
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