UCbase is a database of
ultraconserved sequences (UCRs or UCEs) that were first described by Bejerano, G. et al.
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.
The first release of UCbase was published by Taccioli, C. et al. in 2009.
Recent updates include new annotation based on hg19 Human genome, information about disorders related to the chromosome coordinates using the
SNOMED CT
SNOMED CT or SNOMED Clinical Terms is a systematically organized computer-processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. SNOMED CT is considered to be the mo ...
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 the
UCSC Genome Browser
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate spec ...
. 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
[{{cite journal , last=Lomonaco, first=Vincenzo, author2=Martoglia R , author3=Mandreoli F , author4=Anderlucci L , author5=Emmett W , author6=Bicciato S , author7=Taccioli C. , date=Jan 2009, title=UCbase 2.0: ultraconserved sequences database (2014 update)., journal = ]Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...
, pages=bau062, pmid = 24951797, doi=10.1093/database/bau062 , volume=2014 , pmc=4064129 and is accessible at http://ucbase.unimore.it
See also
*
Sequence conservation
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ...
References
External links
* http://ultraconserved.org
Conservation biology
Computational phylogenetics
Genetics databases
Molecular genetics
Nucleic acids
Population genetics