Database for Identifying Clusters of Short Interspersed Repeats in 3'-Untranslated Regions

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Contents 1 Database Description 2 Authors 3 External Links 4 Contact Email 5 Paper

[edit] Database Description

A Database for Identifying Clusters of Short Interspersed Repeats in 3'-Untranslated Regions

3’-UTR SIRF is a searchable database designed to identify mRNAs from seven vertebrate species with clusters of short, but specific repeats in their 3’-untranslated region (3’-UTR). This site can be used to help identify RNA localization signals, RNA stability elements, miRNA binding sites, or possibly other translational control elements. The database was created by running the program REPFIND (http://zlab.bu.edu/repfind/index.shtml) on the 3’ UTRs of all genes available in the Mammalian Gene Collection (MGC) at NCBI (http://mgc.nci.nih.gov/). The MGC was chosen because it contains almost half of the known human genes, and its cDNA sequences are full-length and well annotated. All repeats from 3-255 nucleotides in length with P-values less than 10-4 were stored in the 3’-UTR SIRF database, and the website allows the rapid identification of genes containing user-defined classes of repeated motifs in their 3’ UTRs.

[edit] Authors

Benjamin B Andken

In Lim

Gary Benson

John J Vincent

Matthew T Ferenc

Bianca Heinrich

Larissa A Jarzylo

Heng-Ye Man

James O Deshler

[edit] External Links

3'-UTRSIRF

[edit] Contact Email

[edit] Paper

BMC Bioinformatics 2007, 8:274