{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:23:47Z","timestamp":1761488627678},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2011,2,1]],"date-time":"2011-02-01T00:00:00Z","timestamp":1296518400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Med Biol Eng Comput"],"published-print":{"date-parts":[[2011,4]]},"DOI":"10.1007\/s11517-011-0732-4","type":"journal-article","created":{"date-parts":[[2011,1,31]],"date-time":"2011-01-31T15:30:39Z","timestamp":1296487839000},"page":"463-472","source":"Crossref","is-referenced-by-count":18,"title":["Characterization and prediction of mRNA polyadenylation sites in human genes"],"prefix":"10.1007","volume":"49","author":[{"given":"Tzu-Hao","family":"Chang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li-Ching","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Ting","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsien-Da","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baw-Jhiune","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kuang-Fu","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorng-Tzong","family":"Horng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,2,1]]},"reference":[{"issue":"8","key":"732_CR1","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1093\/nar\/30.8.1842","volume":"30","author":"GK Arhin","year":"2002","unstructured":"Arhin GK et al (2002) Downstream sequence elements with different affinities for the hnRNP H\/H\u2019 protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res 30(8):1842\u20131850","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"732_CR2","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1101\/gr.10.7.1001","volume":"10","author":"E Beaudoing","year":"2000","unstructured":"Beaudoing E et al (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res 10(7):1001\u20131010","journal-title":"Genome Res"},{"issue":"6","key":"732_CR3","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1007\/s002510100358","volume":"53","author":"CL Bennett","year":"2001","unstructured":"Bennett CL et al (2001) A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA\u2013\u00a0>\u00a0AAUGAA) leads to the IPEX syndrome. Immunogenetics 53(6):435\u2013439","journal-title":"Immunogenetics"},{"issue":"18","key":"732_CR4","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/bti589","volume":"21","author":"JM Brockman","year":"2005","unstructured":"Brockman JM et al (2005) PACdb: polya cleavage site and 3\u2032-UTR database. Bioinformatics 21(18):3691\u20133693","journal-title":"Bioinformatics"},{"issue":"6","key":"732_CR5","doi-asserted-by":"crossref","first-page":"3340","DOI":"10.1128\/JVI.65.6.3340-3343.1991","volume":"65","author":"PH Brown","year":"1991","unstructured":"Brown PH, Tiley LS, Cullen BR (1991) Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences. J Virol 65(6):3340\u20133343","journal-title":"J Virol"},{"issue":"10","key":"732_CR6","doi-asserted-by":"crossref","first-page":"4248","DOI":"10.1128\/MCB.9.10.4248","volume":"9","author":"S Carswell","year":"1989","unstructured":"Carswell S, Alwine JC (1989) Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences. Mol Cell Biol 9(10):4248\u20134258","journal-title":"Mol Cell Biol"},{"issue":"11","key":"732_CR7","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/S0968-0004(00)89102-1","volume":"20","author":"CY Chen","year":"1995","unstructured":"Chen CY, Shyu AB (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci 20(11):465\u2013470","journal-title":"Trends Biochem Sci"},{"issue":"19","key":"732_CR8","doi-asserted-by":"crossref","first-page":"2320","DOI":"10.1093\/bioinformatics\/btl394","volume":"22","author":"Y Cheng","year":"2006","unstructured":"Cheng Y, Miura RM, Tian B (2006) Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22(19):2320\u20132325","journal-title":"Bioinformatics"},{"issue":"21","key":"732_CR9","doi-asserted-by":"crossref","first-page":"2755","DOI":"10.1101\/gad.11.21.2755","volume":"11","author":"DF Colgan","year":"1997","unstructured":"Colgan DF, Manley JL (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev 11(21):2755\u20132766","journal-title":"Genes Dev"},{"issue":"Web Server issu","key":"732_CR10","doi-asserted-by":"crossref","first-page":"W135","DOI":"10.1093\/nar\/gkh449","volume":"32","author":"Y Ding","year":"2004","unstructured":"Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32(Web Server issue):W135\u2013W141","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"732_CR11","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/ng578","volume":"28","author":"NH Gehring","year":"2001","unstructured":"Gehring NH et al (2001) Increased efficiency of mRNA 3\u2032 end formation: a new genetic mechanism contributing to hereditary thrombophilia. Nat Genet 28(4):389\u2013392","journal-title":"Nat Genet"},{"issue":"24","key":"732_CR12","doi-asserted-by":"crossref","first-page":"14055","DOI":"10.1073\/pnas.96.24.14055","volume":"96","author":"JH Graber","year":"1999","unstructured":"Graber JH et al (1999) In silico detection of control signals: mRNA 3\u2032-end-processing sequences in diverse species. Proc Natl Acad Sci USA 96(24):14055\u201314060","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"732_CR13","doi-asserted-by":"crossref","first-page":"2565","DOI":"10.1093\/nar\/gki544","volume":"33","author":"T Hall-Pogar","year":"2005","unstructured":"Hall-Pogar T et al (2005) Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res 33(8):2565\u20132579","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"732_CR14","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1093\/nar\/gkg599","volume":"31","author":"IL Hofacker","year":"2003","unstructured":"Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13):3429\u20133431","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"732_CR15","doi-asserted-by":"crossref","first-page":"D165","DOI":"10.1093\/nar\/gkl870","volume":"35","author":"JY Lee","year":"2007","unstructured":"Lee JY et al (2007) PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 35(Database issue):D165\u2013D168","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"732_CR16","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2164-4-7","volume":"4","author":"M Legendre","year":"2003","unstructured":"Legendre M, Gautheret D (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics 4(1):7","journal-title":"BMC Genomics"},{"key":"732_CR17","first-page":"84","volume":"14","author":"H Liu","year":"2003","unstructured":"Liu H et al (2003) An in-silico method for prediction of polyadenylation signals in human sequences. Genome Inform 14:84\u201393","journal-title":"Genome Inform"},{"issue":"1\u20132","key":"732_CR18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0303-7207(02)00044-8","volume":"190","author":"CC MacDonald","year":"2002","unstructured":"MacDonald CC, Redondo JL (2002) Reexamining the polyadenylation signal: were we wrong about AAUAAA? Mol Cell Endocrinol 190(1\u20132):1\u20138","journal-title":"Mol Cell Endocrinol"},{"issue":"22","key":"732_CR19","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1093\/nar\/29.22.4724","volume":"29","author":"TJ Macke","year":"2001","unstructured":"Macke TJ et al (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29(22):4724\u20134735","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"732_CR20","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gki021","volume":"33","author":"F Mignone","year":"2005","unstructured":"Mignone F et al (2005) UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 33(Database issue):D141\u2013D146","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"732_CR21","doi-asserted-by":"crossref","first-page":"3809","DOI":"10.1002\/j.1460-2075.1995.tb00050.x","volume":"14","author":"A Moreira","year":"1995","unstructured":"Moreira A et al (1995) Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved. EMBO J 14(15):3809\u20133819","journal-title":"EMBO J"},{"issue":"45","key":"732_CR22","doi-asserted-by":"crossref","first-page":"42733","DOI":"10.1074\/jbc.M208070200","volume":"277","author":"BJ Natalizio","year":"2002","unstructured":"Natalizio BJ et al (2002) Upstream elements present in the 3\u2032-untranslated region of collagen genes influence the processing efficiency of overlapping polyadenylation signals. J Biol Chem 277(45):42733\u201342740","journal-title":"J Biol Chem"},{"issue":"1","key":"732_CR23","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1093\/nar\/29.1.137","volume":"29","author":"KD Pruitt","year":"2001","unstructured":"Pruitt KD, Maglott DR (2001) RefSeq and locuslink: NCBI gene-centered resources. Nucleic Acids Res 29(1):137\u2013140","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"732_CR24","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/0092-8674(86)90341-7","volume":"46","author":"G Shaw","year":"1986","unstructured":"Shaw G, Kamen R (1986) A conserved AU sequence from the 3\u2032 untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell 46(5):659\u2013667","journal-title":"Cell"},{"issue":"1\u20132","key":"732_CR25","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S0378-1119(99)00104-3","volume":"231","author":"JE Tabaska","year":"1999","unstructured":"Tabaska JE, Zhang MQ (1999) Detection of polyadenylation signals in human DNA sequences. Gene 231(1\u20132):77\u201386","journal-title":"Gene"},{"issue":"1","key":"732_CR26","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1093\/nar\/gki158","volume":"33","author":"B Tian","year":"2005","unstructured":"Tian B et al (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33(1):201\u2013212","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"732_CR27","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1073\/pnas.88.6.2108","volume":"88","author":"A Valsamakis","year":"1991","unstructured":"Valsamakis A et al (1991) The human immunodeficiency virus type 1 polyadenylylation signal: a 3\u2019 long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. Proc Natl Acad Sci USA 88(6):2108\u20132112","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"732_CR28","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/0167-4781(94)00248-2","volume":"1261","author":"E Wahle","year":"1995","unstructured":"Wahle E (1995) 3\u2032-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta 1261(2):183\u2013194","journal-title":"Biochim Biophys Acta"},{"issue":"3","key":"732_CR29","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1101\/gr.3109605","volume":"15","author":"J Yan","year":"2005","unstructured":"Yan J, Marr TG (2005) Computational analysis of 3\u2032-ends of ESTs shows four classes of alternative polyadenylation in human mouse, and rat. Genome Res 15(3):369\u2013375","journal-title":"Genome Res"},{"issue":"10","key":"732_CR30","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2004-5-10-r74","volume":"5","author":"G Yeo","year":"2004","unstructured":"Yeo G et al (2004) Variation in alternative splicing across human tissues. Genome Biol 5(10):R74","journal-title":"Genome Biol"},{"issue":"5","key":"732_CR31","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1093\/nar\/gkg241","volume":"31","author":"MI Zarudnaya","year":"2003","unstructured":"Zarudnaya MI et al (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 31(5):1375\u20131386","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"732_CR32","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/bib\/1.4.331","volume":"1","author":"MQ Zhang","year":"2000","unstructured":"Zhang MQ (2000) Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform 1(4):331\u2013342","journal-title":"Brief Bioinform"},{"issue":"12","key":"732_CR33","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1101\/gr.1679003","volume":"13","author":"XH Zhang","year":"2003","unstructured":"Zhang XH et al (2003) Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome Res 13(12):2637\u20132650","journal-title":"Genome Res"},{"issue":"9","key":"732_CR34","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1093\/bioinformatics\/16.9.799","volume":"16","author":"A Zien","year":"2000","unstructured":"Zien A et al (2000) Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics 16(9):799\u2013807","journal-title":"Bioinformatics"}],"container-title":["Medical &amp; Biological Engineering &amp; Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11517-011-0732-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11517-011-0732-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11517-011-0732-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,16]],"date-time":"2020-06-16T04:23:51Z","timestamp":1592281431000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11517-011-0732-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,1]]},"references-count":34,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2011,4]]}},"alternative-id":["732"],"URL":"https:\/\/doi.org\/10.1007\/s11517-011-0732-4","relation":{},"ISSN":["0140-0118","1741-0444"],"issn-type":[{"value":"0140-0118","type":"print"},{"value":"1741-0444","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,1]]}}}