{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T08:28:23Z","timestamp":1779352103089,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"3-4","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":6005,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"name":"PICB"},{"name":"DFG-funded"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.<\/jats:p>","DOI":"10.1016\/s1672-0229(08)60006-6","type":"journal-article","created":{"date-parts":[[2008,2,11]],"date-time":"2008-02-11T12:15:33Z","timestamp":1202732133000},"page":"187-195","source":"Crossref","is-referenced-by-count":19,"title":["U7 snRNAs: A Computational Survey"],"prefix":"10.1093","volume":"5","author":[{"given":"Manja","family":"Marz","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Leipzig , Leipzig, D-04107 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Axel","family":"Mosig","sequence":"additional","affiliation":[{"name":"Department of Combinatorics and Geometry, CAS\/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, 200031 , China"},{"name":"Max Planck Institute for Mathematics in the Sciences , Leipzig, D-04103 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B\u00e4rbel M.R.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Mathematics in the Sciences , Leipzig, D-04103 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Leipzig , Leipzig, D-04107 , Germany"},{"name":"Interdisciplinary Center for Bioinformatics, University of Leipzig , Leipzig, D-04107 , Germany"},{"name":"Fraunhofer Institute for Cell Therapy and Immunology , Leipzig, D-04103 , Germany"},{"name":"Department of Theoretical Chemistry, University of Vienna , Vienna, A-1090 , Austria"},{"name":"Santa Fe Institute , Santa Fe, NM, 87501 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,8]]},"reference":[{"key":"2024051008240097000_bib1","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1126\/science.2825355","article-title":"Identification of the human U7 snRNP as one of several factors involved in the 3\u2032 end maturation of histone premessenger RNAs","volume":"238","author":"Mowry","year":"1987","journal-title":"Science"},{"key":"2024051008240097000_bib2","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.ceb.2005.04.010","article-title":"Metazoan replication-dependent histone mRNAs: a distinct set of RNA polymerase II transcripts","volume":"17","author":"Marzluff","year":"2005","journal-title":"Curr. Opin. Cell Biol."},{"key":"2024051008240097000_bib3","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/BF00326431","article-title":"The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes","volume":"28","author":"Fabry","year":"1995","journal-title":"Curr. Genet."},{"key":"2024051008240097000_bib4","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1261\/rna.76006","article-title":"Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein","volume":"12","author":"Townley-Tilson","year":"2006","journal-title":"RNA"},{"key":"2024051008240097000_bib5","doi-asserted-by":"crossref","first-page":"10989","DOI":"10.1128\/MCB.25.24.10989-11004.2005","article-title":"Specific sequence features, recognized by the SMN complex, identify snRNAs and determine their fate as snRNPs","volume":"25","author":"Golembe","year":"2005","journal-title":"Mol. Cell. Biol."},{"key":"2024051008240097000_bib6","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1261\/rna.5143303","article-title":"Evolutionary conservation of the U7 small nuclear ribonucleoprotein in Drosophila melanogaster","volume":"9","author":"Azzouz","year":"2003","journal-title":"RNA"},{"key":"2024051008240097000_bib7","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1101\/gad.274403","article-title":"Unique Sm core structure of U7 snRNPs: assembly by a specialized SMN complex and the role of a new component, Lsm11, in histone RNA processing","volume":"17","author":"Pillai","year":"2003","journal-title":"Genes. Dev."},{"key":"2024051008240097000_bib8","doi-asserted-by":"crossref","first-page":"2560","DOI":"10.1007\/s00018-004-4190-0","article-title":"The special Sm core structure of the U7 snRNP: far-reaching significance of a small nuclear ribonucleoprotein","volume":"61","author":"Sch\u00fcmperli","year":"2004","journal-title":"Cell. Mol. Life Sci."},{"key":"2024051008240097000_bib9","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nsmb1075","article-title":"In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site","volume":"13","author":"Kolev","year":"2006","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2024051008240097000_bib10","doi-asserted-by":"crossref","first-page":"4987","DOI":"10.1093\/nar\/gkl666","article-title":"Binding of human SLBP on the 3\u2032-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring","volume":"34","author":"Jaeger","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2024051008240097000_bib11","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1007\/s000180300047","article-title":"U7 snRNAs induce correction of mutated dystrophin pre-mRNA by exon skipping","volume":"60","author":"Brun","year":"2003","journal-title":"Cell. Mol. Life Sci."},{"key":"2024051008240097000_bib12","doi-asserted-by":"crossref","first-page":"1796","DOI":"10.1126\/science.1104297","article-title":"Rescue of dystrophic muscle through U7 snRNA-mediated exon skipping","volume":"306","author":"Goyenvalle","year":"2004","journal-title":"Science"},{"key":"2024051008240097000_bib13","first-page":"1518","article-title":"Structural and functional characterization of mouse U7 small nuclear RNA active in 3\u2032 processing of histone pre-mRNA","volume":"8","author":"Soldati","year":"1988","journal-title":"Mol. Cell. Biol."},{"key":"2024051008240097000_bib14","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/0167-4781(91)90167-K","article-title":"Isolation of an active gene and of two pseudogenes for mouse U7 small nuclear RNA","volume":"1088","author":"Gruber","year":"1991","journal-title":"Biochim. Biophys. Acta"},{"key":"2024051008240097000_bib15","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/0378-1119(92)90514-P","article-title":"A transcriptional analysis of the gene encoding mouse U7 small nuclear RNA","volume":"116","author":"Phillips","year":"1992","journal-title":"Gene"},{"key":"2024051008240097000_bib16","doi-asserted-by":"crossref","first-page":"401","DOI":"10.3109\/10425179109020796","article-title":"Sequence and expression of a mouse U7 snRNA type II pseudogene","volume":"1","author":"Phillips","year":"1991","journal-title":"DNA Seq."},{"key":"2024051008240097000_bib17","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1006\/excr.1996.0372","article-title":"More Sm snRNAs from vertebrate cells","volume":"229","author":"Yu","year":"1996","journal-title":"Exp. Cell Res."},{"key":"2024051008240097000_bib18","doi-asserted-by":"crossref","first-page":"2801","DOI":"10.1002\/j.1460-2075.1984.tb02212.x","article-title":"The cDNA sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA processing","volume":"3","author":"Strub","year":"1984","journal-title":"EMBO J."},{"key":"2024051008240097000_bib19","doi-asserted-by":"crossref","first-page":"3243","DOI":"10.1073\/pnas.83.10.3243","article-title":"Analysis of a sea urchin gene cluster coding for the small nuclear U7 RNA, a rare RNA species implicated in the 3\u2032 editing of histone precursor mRNAs","volume":"83","author":"De Lorenzi","year":"1986","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008240097000_bib20","first-page":"1076","article-title":"Functional analysis of the sea urchin U7 small nuclear RNA","volume":"8","author":"Gilmartin","year":"1988","journal-title":"Mol. Cell. Biol."},{"key":"2024051008240097000_bib21","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1002\/j.1460-2075.1989.tb03408.x","article-title":"In vivo and in vitro expression of U7 snRNA genes: cis- and trans-acting elements required for RNA polymerase II-directed transcription","volume":"8","author":"Southgate","year":"1989","journal-title":"EMBO J."},{"key":"2024051008240097000_bib22","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/0167-4781(92)90104-8","article-title":"Analysis of a gene cluster coding for the Xenopus laevis U7 snRNA","volume":"1131","author":"Phillips","year":"1992","journal-title":"Biochim. Biophys. Acta"},{"key":"2024051008240097000_bib23","doi-asserted-by":"crossref","first-page":"301S","DOI":"10.1042\/bst020301s","article-title":"The U7 small nuclear RNA genes of Xenopus borealis","volume":"20","author":"Watkins","year":"1992","journal-title":"Biochem. Soc. Trans."},{"key":"2024051008240097000_bib24","doi-asserted-by":"crossref","first-page":"6257","DOI":"10.1073\/pnas.90.13.6257","article-title":"U7 small nuclear RNA in C snurposomes of the Xenopus germinal vesicle","volume":"90","author":"Wu","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008240097000_bib25","doi-asserted-by":"crossref","first-page":"9422","DOI":"10.1073\/pnas.1533509100","article-title":"Cloning and characterization of the Drosophila U7 small nuclear RNA","volume":"100","author":"Dominski","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008240097000_bib26","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.gene.2004.01.021","article-title":"Characterization of snRNA and snRNA-type genes in the pufferfish Fugu rubripes","volume":"330","author":"Myslinksi","year":"2004","journal-title":"Gene"},{"key":"2024051008240097000_bib27","doi-asserted-by":"crossref","first-page":"4208","DOI":"10.1093\/nar\/27.21.4208","article-title":"Construct: a tool for thermodynamic controlled prediction of conserved secondary structure","volume":"27","author":"L\u00fcck","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2024051008240097000_bib28","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.thbio.2005.01.002","article-title":"Evolutionary patterns of non-coding RNAs","volume":"123","author":"Bompf\u00fcnewerer","year":"2005","journal-title":"Theory Biosci."},{"key":"2024051008240097000_bib29","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024051008240097000_bib30","doi-asserted-by":"crossref","first-page":"26733","DOI":"10.1074\/jbc.R100032200","article-title":"Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription","volume":"276","author":"Hernandez","year":"2001","journal-title":"J. Biol. Chem."},{"key":"2024051008240097000_bib31","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1093\/nar\/gkl982","article-title":"Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity","volume":"35","author":"Hernandez","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2024051008240097000_bib32","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/0378-1119(90)90378-5","article-title":"Structures of four human pseudogenes for U7 small nuclear RNA","volume":"95","author":"Soldati","year":"1990","journal-title":"Gene"},{"key":"2024051008240097000_bib33","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1261\/rna.2179305","article-title":"Differences and similarities between Drosophila and mammalian 3\u2032 end processing of histone pre-mRNAs","volume":"11","author":"Dominski","year":"2005","journal-title":"RNA"},{"key":"2024051008240097000_bib34","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/S1672-0229(06)60017-X","article-title":"Fragrep: an efficient search tool for fragmented patterns in genomic sequences","volume":"4","author":"Mosig","year":"2006","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024051008240097000_bib35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0030056","article-title":"Query-dependent banding (QDB) for faster RNA similarity searches","volume":"3","author":"Nawrocki","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2024051008240097000_bib36","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/bioinformatics\/15.3.211","article-title":"DIALIGN2: improvement of the segment-to-segment approach to multiple sequence alignment","volume":"15","author":"Morgenstern","year":"1999","journal-title":"Bioinformatics"},{"key":"2024051008240097000_bib37","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2024051008240097000_bib38","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/bth489","article-title":"RALEE\u2014RNA alignment editor in Emacs","volume":"21","author":"Griffiths-Jones","year":"2005","journal-title":"Bioinformatics"},{"key":"2024051008240097000_bib39","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/S0022-2836(02)00308-X","article-title":"Secondary structure prediction for aligned RNA sequences","volume":"319","author":"Hofacker","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2024051008240097000_bib40","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022908600066?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022908600066?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/5\/3-4\/187\/57483312\/gpb_5_3-4_187.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/5\/3-4\/187\/57483312\/gpb_5_3-4_187.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T08:25:08Z","timestamp":1715329508000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/5\/3-4\/187\/7210714"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,12,1]]},"references-count":40,"journal-issue":{"issue":"3-4","published-print":{"date-parts":[[2007,12,1]]}},"URL":"https:\/\/doi.org\/10.1016\/s1672-0229(08)60006-6","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2007,12]]},"published":{"date-parts":[[2007,12,1]]}}}