UCbase

{{Update|reason=Database no longer exists|date=June 2024}}

{{infobox biodatabase

|title = UCbase 2.0

|logo =File:Database.png

|description =ultraconserved sequences database.

|scope =

|organism =Homo sapiens
Mus musculus
Rattus norvegicus

|center =The Ohio State University

|laboratory = Professor Carlo M. Croce, MD

|author = Professor Cristian Taccioli, Ph.D

|citation = Taccioli, C. et al. (2014)

|released = 2014

|standard =

|format =

|url = http://ucbase.unimore.it

|download =

|webservice =

|sql =

|sparql =

|webapp =

|standalone =

|license =

|versioning =

|frequency = 6 months

|curation =

|bookmark =

|version=

}}UCbase is a database of ultraconserved sequences (UCRs or UCEs) that were first described by Bejerano, G. et al.{{cite journal | last=Bejerano|first=Gill|author2=Pheasant M |author3=Makunin I |author4=Stephen S |author5=Kent WJ |author6=Mattick JS |author7=Haussler D. |date=May 2004|title=Ultraconserved elements in the human genome|journal = Science|volume=304|issue=5675|pages=1321–5| pmid = 15131266|doi=10.1126/science.1098119|bibcode=2004Sci...304.1321B|citeseerx=10.1.1.380.9305|s2cid=2790337}} 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.{{cite journal|vauthors = Calin GA, 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|title=Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas.|journal=Cancer Cell|date=Sep 2007|volume=12|issue=3|pages=215–29|pmid=17785203|doi=10.1016/j.ccr.2007.07.027|doi-access=free}} The first release of UCbase was published by Taccioli, C. et al. in 2009.{{cite journal |vauthors=Taccioli C, Fabbri E, Visone R, Volinia S, Calin GA, Fong LY, Gambari R, Bottoni A, Acunzo M, Hagan J, Iorio MV, Piovan C, Romano G, Croce CM |date=Jan 2009|title=UCbase & miRfunc: a database of ultraconserved sequences and microRNA function|journal = Nucleic Acids Res.|volume=37|issue=Database issue|pages=D41–8| pmid = 18945703|doi=10.1093/nar/gkn702|pmc=2686429}} 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 the 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.{{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|pages=bau062| pmid = 24951797|doi=10.1093/database/bau062 |volume=2014 |pmc=4064129}}