UTRdb 2.0 is an updated version of the specialized database UTRdb, which focuses on the 5' and 3'
untranslated region
In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the Directionality (molecular biology), 5' side, it is called the Five prime ...
s (UTRs) of eukaryotic
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
s. These UTRs play essential roles in the
post-transcriptional regulation
Post-transcriptional regulation is the control of gene expression at the RNA level. It occurs once the RNA polymerase has been attached to the gene's promoter and is synthesizing the nucleotide sequence. Therefore, as the name indicates, it occur ...
of
gene expression
Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
by influencing various processes, including nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and mRNA stability. Since its launch in 1996, UTRdb has been a valuable resource for researchers studying UTR sequences and their functional implications.
Content and features
UTRdb 2.0 contains a comprehensive collection of over 26 million entries, derived from more than 6 million genes across 573 species. The database is enriched with a curated set of functional annotations to enhance the understanding of UTR function. These annotations include:
* CAGE tags: marking the completeness of 5' UTRs
* PolyA signals: indicating the completeness of 3' UTRs
* uORFs and IRES: annotating upstream open reading frames (uORFs) and internal ribosome entry sites (IRES) in 5' UTRs
* miRNA targets: annotating experimentally validated miRNA targets in 3' UTRs
* Evolutionarily conserved blocks: identifying conserved regions across species
* Rfam motifs: recognizing RNA motifs associated with function
* ADAR-mediated RNA editing: annotating RNA editing events mediated by the ADAR enzyme
* m6A modifications: marking mRNA modifications related to N6-methyladenosine
Web interface and access
UTRdb 2.0 provides a flexible web interface that allows users to select and retrieve subsets of UTRs based on various criteria. This tool offers comprehensive download options to access the data for further analysis.
References
External links
UTRdb
Biological databases
RNA
Gene expression
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