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Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in<jats:italic>Xenopus<\/jats:italic>oocytes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Description<\/jats:title><jats:p>In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (<jats:bold><jats:underline>S<\/jats:underline><\/jats:bold>hort<jats:bold><jats:underline>I<\/jats:underline><\/jats:bold>nterspersed<jats:bold><jats:underline>R<\/jats:underline><\/jats:bold>epeat<jats:bold><jats:underline>F<\/jats:underline><\/jats:bold>inder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by<jats:italic>in situ<\/jats:italic>hybridization. Our results show that two candidate CAC-rich (<jats:italic>Syntaxin 1B<\/jats:italic>and<jats:italic>Tubulin \u03b24<\/jats:italic>) and two candidate CAG-rich (<jats:italic>Sec61\u03b1<\/jats:italic>and<jats:italic>Syntaxin 1A<\/jats:italic>) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons.<jats:italic>In situ<\/jats:italic>hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing<jats:italic>cis<\/jats:italic>-regulatory information located in 3'-UTRs.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-8-274","type":"journal-article","created":{"date-parts":[[2007,8,2]],"date-time":"2007-08-02T18:15:50Z","timestamp":1186078550000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions"],"prefix":"10.1186","volume":"8","author":[{"given":"Benjamin B","family":"Andken","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"In","family":"Lim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary","family":"Benson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John J","family":"Vincent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew T","family":"Ferenc","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bianca","family":"Heinrich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Larissa A","family":"Jarzylo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heng-Ye","family":"Man","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James O","family":"Deshler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,7,30]]},"reference":[{"key":"1646_CR1","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1101\/gad.8.13.1561","volume":"8","author":"GS Huh","year":"1994","unstructured":"Huh GS, Hynes RO: Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. 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