Welcome to the UCbase 2.0

Ultraconserved elements (UCRs), that were first described by Bejerano et al. in 2004 (Science. 2004;304:1321-5), are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases. UCRs 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 in NAR Journal in 2009 by Taccioli et al. UCRs chromosome coordinates are now updated with the last Human Genome (hg19/GRCh37) chromosome Information. UCbase 2.0 is directly linked to UCSC Genome Browser. The last version of UCbase (2.0) has been published in 2014 in "Database: The Journal of Biological of Databases and curation

05/08 2014

Things to Know

  • Why UCbase?

    UCbase arises from the need to recover updated information about ultraconserved sequences as published by Bejerano et al in 2004 (Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, et al. Ultraconserved elements in the human genome. Science. 2004).

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  • More info about Ultraconserved sequences

    Ultraconserved elements (UCRs) are genomic sequences that share 100% identity among three mammal species: human, mouse and rat. UCRs were first described in a wonderful manuscript by Gil Bejerano et al. (2004) from David Haussler’s group and subsequently identified in several classes of organisms outside the group of original taxa (Siepel et al. 2005) used to identify these genomic elements. The 27-way vertebrate genome alignment (Miller et al. 2007) identified additional regions of high conservation.

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  • Old version of UCbase

    [Nucleic Acids Res. 2009 Jan;37:D41-8. doi: 10.1093/nar/gkn702. Epub 2008 Oct 22]The first release of UCbase was published by Taccioli 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 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 UCRs 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 will be accessible in September 2013.

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    UCbase manual is available in pdf format.

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