期刊
GENOMICS PROTEOMICS & BIOINFORMATICS
卷 19, 期 4, 页码 602-610出版社
ELSEVIER
DOI: 10.1016/j.gpb.2021.09.002
关键词
Ribosome profiling; Small open reading frame; Upstream open reading frame; Variants; Disease
资金
- National Key R&D Program of China [2016YFC0901702, 81902519, 91940306, 31871294]
- National Natural Science Foundation of China [31701117, 31970647, 2017YFC0907503, 2016YFC0901002, 2018YFA0106901]
- Strategic Priority Research Program of Chinese Academy of Sciences [XDB38040300]
- 13th Five-year Informatization Plan of Chinese Academy of Sciences [2019FY100102]
- Special Investigation on Science and Technology Basic Resources, Ministry of Science and Technology, China [2017YFC0907503]
- National Genomics Data Center, China
- [XXH13505-05)]
Small proteins, translated from small open reading frames (sORFs), have been recognized for their diverse functions in recent years. However, systematic annotation of small proteins is still insufficient. SmProt offers a curated database of unique small proteins for free access, with increased data volume and updated features.
Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cere-visiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human micro -biomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.
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