UCbase
 | |
|---|---|
| Content | |
| Description | ultraconserved sequences database. |
| Organisms |
Homo sapiens Mus musculus Rattus norvegicus |
| Contact | |
| Research center | The Ohio State University |
| Laboratory | Professor Carlo M. Croce, MD |
| Authors | Dr Cristian Taccioli, Ph.D |
| Primary citation | Taccioli, C. et al. (2014)[1] |
| Release date | 2014 |
| Access | |
| Website | http://ucbase.unimore.it |
| Tools | |
| Miscellaneous | |
| Data release frequency | 6 months |
UCbase is a database of ultraconserved sequences (UCRs or UCEs) that were first described by Bejerano, G. et al.[2] in 2004. They are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases. They are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs.[3] The first release of UCbase was published by Taccioli, C. et al. in 2009.[4] Recent updates include new annotation based on hg19 Human genome, information about disorders related to the chromosome coordinates using the SNOMED CT classification, a query tool to search for SNPs, and a new text box to directly interrogate the database using a MySQL interface. Moreover, a sequence comparison tool allows the researchers to match selected sequences against ultraconserved elements located in genomic regions involved in specific disorders. To facilitate the interactive, visual interpretation of UCR chromosomal coordinates, the authors have implemented the graph visualization feature of UCbase creating a link to UCSC genome browser. UCbase 2.0 does not provide microRNAs (miRNAs) information anymore focusing only on UCRs. The official release of UCbase 2.0 was published in 2014[1] and is accessible at http://ucbase.unimore.it
See also
- Sequence conservation
References
- ↑ 1.0 1.1 Lomonaco, Vincenzo; Martoglia R; Mandreoli F; Anderlucci L; Emmett W; Bicciato S; Taccioli C. (Jan 2009). "UCbase 2.0: ultraconserved sequences database (2014 update).". Database: The Journal of Biological Databases and Curation 2014: 1–8. doi:10.1093/database/bau062. PMC 4064129. PMID 24951797.
- ↑ Bejerano, Gill; Pheasant M; Makunin I; Stephen S; Kent WJ; Mattick JS; Haussler D. (May 2004). "Ultraconserved elements in the human genome". Science 304 (5675): 1321–5. doi:10.1126/science.1098119. PMID 15131266.
- ↑ Calin, George Adrian; Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, Shimizu M, Tili E, Rossi S, Taccioli C, Pichiorri F, Liu X, Zupo S, Herlea V, Gramantieri L, Lanza G, Alder H, Rassenti L, Volinia S, Schmittgen TD, Kipps TJ, Negrini M, Croce CM (2007). "Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas". Cancer Cell 12 (3): 215–29. doi:10.1016/j.ccr.2007.07.027. PMID 17785203.
- ↑ Taccioli, Cristian; Fabbri Enrica, Visone Rosa, Volinia Stefano, Calin George A, Fong Louise Y, Gambari Roberto, Bottoni Arianna, Acunzo Mario, Hagan John, Iorio Marilena V, Piovan Claudia, Romano Giulia, Croce Carlo Maria (Jan 2009). "UCbase & miRfunc: a database of ultraconserved sequences and microRNA function". Nucleic Acids Res. 37 (Database issue): D41–8. doi:10.1093/nar/gkn702. PMC 2686429. PMID 18945703.