{"search_session":{},"preferences":{"l":"ru","queryLanguage":"ru"},"patentId":"018-168-608-143-193","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"018-168-608-143-193","entityRefType":"PATENT"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":8906,"type":"PATENT","title":"Univ Pennsylvania Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":24238,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8221,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
Search applicants and owners= \"Univ Pennsylvania\", \"Pennsylvania Univ\", \"Univ Penns*\", \"Penn* Univ\", \"University of Pennsylvania\", \"Pennsylvania University\".
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Search applicants and owners= \"Univ Pennsylvania\", \"Pennsylvania Univ\", \"Univ Penns*\", \"Penn* Univ\", \"University of Pennsylvania\", \"Pennsylvania University\".
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preparing RNase footprinting and control libraries;\n
identifying candidate protein binding sites within the RNase footprinting library; and\n
identifying sequence level motifs within the candidate protein binding sites."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein preparing an RNase footprinting libarary includes:\n
crosslinking at least one cell;\n
obtaining a sample from the at least one cell;\n
treating a first fraction of the sample with single-stranded RNase;\n
treating a second fraction of the sample with double-stranded RNase;\n
treating the first fraction and the second fraction with a protease or proteinase;\n
isolating RNA from the first fraction and the second fraction; and\n
preparing a strand specific sequence library."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein preparing an RNase footprinting control library includes:\n
crosslinking at least one cell;\n
obtaining a sample from the at least one cell;\n
treating a first fraction of the sample with protease or proteinase;\n
treating a second fraction of the sample with protease or proteinase;\n
treating the first fraction of the sample with single-stranded RNase;\n
treating the second fraction of the sample with double-stranded RNase;\n
isolating RNA from the first fraction and the second fraction; and\n
preparing a strand specific sequence library."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 2, wherein obtaining the sample includes lysing the at least one cell to obtain the sample."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 4 further comprising treating the sample with DNase."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 2 further comprising treating the sample with protease or proteinase after RNase treatment."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 2 further comprising treating at least one of the first fraction or the second fraction of the sample with protease or proteinase before RNase treatment."],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 3, wherein obtaining the sample includes lysing the at least one cell to obtain the sample."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8 further comprising treating the sample with DNase."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 3 further comprising treating the sample with protease or proteinase after RNase treatment."],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 3 further comprising treating at least one of the first fraction or the second fraction of the sample with protease or proteinase before RNase treatment."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying candidate protein binding sites includes identifying protein protected sites; and comparing the protein protected sites with previously published protein data."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying sequence level motifs includes selecting a site specific candidate protein binding site from the candidate protein binding sites; and performing a MEME motif search on the site specific candidate protein binding site to identify at least one motif."],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein the site specific candidate binding site is found in the 5′ UTR, the protein coding region, or the 3′ UTR."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13 further comprising validating the at least one motif by a competitive pull-down assay."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["A system for identifying RNA-protein interaction sites comprising:\n
an RNA footprinting database, the RNA footprinting database comprising data associated with an RNA footprinting library; and\n
a processor configured to perform the steps of:\n
identifying candidate protein binding sites within the RNase footprinting library; and\n
identifying sequence level motifs within the candidate protein binding sites."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["A system for identifying RNA-protein interaction sites comprising:\n
one or more processors configured to execute program instructions;\n
a computer-readable medium containing executable instructions that when executed by the one or more processors, cause the system to perform the steps of:\n
accessing an RNase footprinting library;\n
identifying candidate protein binding sites within the RNase footprinting library; and\n
identifying sequence level motifs within the candidate protein binding sites."],"number":17,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 17 further comprising the step of compiling data to obtain the RNase footprinting library."],"number":18,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 17, wherein identifying candidate protein binding sites includes identifying protein protected sites; and comparing the protein protected sites with previously published protein data."],"number":19,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 19 further comprising performing functional analysis of the protein protected sites."],"number":20,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 20, wherein performing functional analysis includes at least one of performing classification and genomic distribution of the protein protected sites; performing conservation analysis of the protein protected sites; comparing the protein protected sites with previously published protein data; or performing SNP association of the protein protected sites."],"number":21,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 19 further comprising performing secondary structure analysis of the protein protected sites."],"number":22,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 17, wherein identifying sequence level motifs includes selecting a site specific candidate protein binding site from the candidate protein binding sites; and performing a MEME motif search on the site specific candidate protein binding site to identify at least one motif."],"number":23,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 23 further comprising performing secondary structure analysis of the at least one motif."],"number":24,"annotation":false,"claim":true,"title":false},{"lines":["A system for identifying secondary structures comprising:\n
one or more processors configured to execute program instructions;\n
a computer-readable medium containing executable instructions that when executed by the one or more processors, cause the computer system to perform the steps of:\n
accessing RNase footprinting and control libraries; and\n
creating secondary structure profiles from the RNase footprinting and control libraries."],"number":25,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 25, wherein the RNase footprinting library includes a first data set comprising ssRNase treated fractions in the presence or absence of bound protein and a second data set comprising dsRNase treated fractions in the presence or absence of bound protein."],"number":26,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 26 further comprising calculating normalized structure scores from the first data set and the second data set."],"number":27,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 27 further comprising creating base pairing profiles from the normalized structure scores."],"number":28,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 28 further comprising determining the background distribution of structure scores."],"number":29,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 27 further comprising determining paired and unpaired nucleotide positions."],"number":30,"annotation":false,"claim":true,"title":false},{"lines":["The system of claim 27 further comprising determining constrained energy-based RNA folding."],"number":31,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying secondary structures comprising:\n
obtaining a first data set comprising ssRNase treated fractions in the presence or absence of bound protein and a second data set comprising dsRNase treated fractions in the presence or absence of protein;\n
calculating normalized structure scores from the first data set and the second data set; and\n
creating a secondary structure model from the normalized structure scores."],"number":32,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 32 further comprising creating base pairing profiles from the normalized structure scores."],"number":33,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying RNA-binding proteins comprising:\n
identifying sequence level motifs;\n
preparing an RNA substrate having an identified sequence level motif;\n
exposing the RNA substrate to a sample containing candidate RNA-binding proteins; and\n
isolating candidate RNA binding proteins interacting with the RNA substrate, wherein an isolated candidate RNA binding protein interacting with the RNA substrate is identified as one of the RNA binding proteins."],"number":34,"annotation":false,"claim":true,"title":false},{"lines":["An isolated nucleic acid molecule comprising a sequence having at least 87.5% identity to one selected from the group consisting of Motif 5-AGAAGGCA, Motif 26-TGGTTAGTACTT [SEQ ID NO: 1], Motif 4-ATCTGATC, Motif 7-GATCTCGGAAG [SEQ ID NO: 2], Motif_UTR—4-GAAGCTAAGC [SEQ ID NO: 3], 3′ UTR C-rich element-GCCCCCTCCCCCCCCCCCCC [SEQ ID NO: 4], 3′ UTR Unknown element-AGCAGAAG, 3′ UTR Unknown hairpin-CAGGCCGTGCTGCTGCCCA [SEQ ID NO: 5], 5′ UTR GGC repeat-GGCGGCGGCGGCGGC [SEQ ID NO: 6], 5′ UTR CAG repeat-CGGCAGCAGCAGCAGAAG [SEQ ID NO: 7], 3′ UTR TG repeat-TGTGTGTGTGTGTGTGTGTG [SEQ ID NO: 8] 5′ UTR Unknown element-AAGATGGCGGC [SEQ ID NO: 9], CDS AAG repeat-AGAAGAAG, and Intronic Unknown element-CTGTAGAA."],"number":35,"annotation":false,"claim":true,"title":false},{"lines":["The isolated nucleic acid of claim 35, wherein the percent identity is 100%."],"number":36,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}