{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T22:06:24Z","timestamp":1784153184463,"version":"3.55.0"},"reference-count":69,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T00:00:00Z","timestamp":1678060800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T00:00:00Z","timestamp":1678060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"BRNS, Department of Atomic energy (DAE), Govt. of India, Mumbai, India","award":["BRNS No. 2013\/37B\/28"],"award-info":[{"award-number":["BRNS No. 2013\/37B\/28"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Biol Rep"],"published-print":{"date-parts":[[2023,5]]},"DOI":"10.1007\/s11033-023-08314-7","type":"journal-article","created":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T15:03:13Z","timestamp":1678114993000},"page":"4105-4117","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy"],"prefix":"10.1007","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4775-5067","authenticated-orcid":false,"given":"Prerna","family":"Giri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dharmendra","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashok","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1642-7733","authenticated-orcid":false,"given":"Bhagyalaxmi","family":"Mohapatra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,3,6]]},"reference":[{"issue":"7","key":"8314_CR1","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1161\/CIRCRESAHA.117.309711","volume":"121","author":"WJ McKenna","year":"2017","unstructured":"McKenna WJ, Maron BJ, Thiene G (2017) Classification, epidemiology, and global burden of cardiomyopathies. Circul Res 121(7):722\u2013730. https:\/\/doi.org\/10.1161\/CIRCRESAHA.117.309711","journal-title":"Circul Res"},{"key":"8314_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10741-021-10125-6","volume":"10","author":"P Giri","year":"2021","unstructured":"Giri P, Mukhopadhyay A, Gupta M, Mohapatra B (2021) Dilated cardiomyopathy: a new insight into the rare but common cause of heart failure. Heart Fail Rev 10:1\u201324. https:\/\/doi.org\/10.1007\/s10741-021-10125-6","journal-title":"Heart Fail Rev"},{"issue":"3","key":"8314_CR3","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/S0014-5793(99)01566-5","volume":"462","author":"AA Komar","year":"1999","unstructured":"Komar AA, Lesnik T, Reiss C (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett 462(3):387\u2013391. https:\/\/doi.org\/10.1016\/S0014-5793(99)01566-5","journal-title":"FEBS Lett"},{"key":"8314_CR4","doi-asserted-by":"publisher","unstructured":"Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 4285\u2013298. https:\/\/doi.org\/10.1038\/nrg775","DOI":"10.1038\/nrg775"},{"key":"8314_CR5","doi-asserted-by":"publisher","unstructured":"Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 132\u201342. https:\/\/doi.org\/10.1038\/nrg2899","DOI":"10.1038\/nrg2899"},{"issue":"23","key":"8314_CR6","doi-asserted-by":"publisher","first-page":"2674","DOI":"10.1161\/01.CIR.101.23.2674","volume":"101","author":"O Zolk","year":"2000","unstructured":"Zolk O, Caroni P, B\u00f6hm M (2000) Decreased expression of the cardiac LIM domain protein MLP in chronic human heart failure. Circulation 101(23):2674\u20132677. https:\/\/doi.org\/10.1161\/01.CIR.101.23.2674","journal-title":"Circulation"},{"issue":"7","key":"8314_CR7","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1016\/S0092-8674(02)01226-6","volume":"111","author":"R Kn\u00f6ll","year":"2002","unstructured":"Kn\u00f6ll R, Hoshijima M, Hoffman HM, Person V, Lorenzen-Schmidt I, Bang ML, Hayashi T, Shiga N, Yasukawa H, Schaper W, McKenna W (2002) The cardiac mechanical stretch sensor machinery involves a Z disc complex that is defective in a subset of human dilated cardiomyopathy. Cell 111(7):943\u2013955. https:\/\/doi.org\/10.1016\/S0092-8674(02)01226-6","journal-title":"Cell"},{"issue":"13","key":"8314_CR8","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","volume":"31","author":"M Zuker","year":"2003","unstructured":"Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406\u20133415. https:\/\/doi.org\/10.1093\/nar\/gkg595","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"8314_CR9","doi-asserted-by":"publisher","first-page":"3026","DOI":"10.1016\/S0021-9258(19)81068-2","volume":"257","author":"JL Bennetzen","year":"1982","unstructured":"Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257(6):3026\u20133031. https:\/\/doi.org\/10.1016\/S0021-9258(19)81068-2","journal-title":"J Biol Chem"},{"key":"8314_CR10","doi-asserted-by":"crossref","unstructured":"Mirsafian H, Mat Ripen A, Singh A, Teo PH, Merican AF, Mohamad SB (2014) A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily. The Scientific World Journal 2014","DOI":"10.1155\/2014\/639682"},{"issue":"3","key":"8314_CR11","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","volume":"15","author":"PM Sharp","year":"1987","unstructured":"Sharp PM, Li WH (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15(3):1281\u20131295. https:\/\/doi.org\/10.1093\/nar\/15.3.1281","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"8314_CR12","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1016\/j.cell.2006.07.031","volume":"126","author":"KC Miranda","year":"2006","unstructured":"Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126(6):1203\u20131217. https:\/\/doi.org\/10.1016\/j.cell.2006.07.031","journal-title":"Cell"},{"key":"8314_CR13","doi-asserted-by":"publisher","unstructured":"Pagani F, Raponi M, Baralle FE (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proceedings of the National Academy of Sciences 102(18):6368-72. https:\/\/doi.org\/10.1073\/pnas.0502288102","DOI":"10.1073\/pnas.0502288102"},{"issue":"2","key":"8314_CR14","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nsmb.2466","volume":"20","author":"S Pechmann","year":"2013","unstructured":"Pechmann S, Frydman J (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat Struct Mol Biol 20(2):237. https:\/\/doi.org\/10.1038\/nsmb.2466","journal-title":"Nat Struct Mol Biol"},{"issue":"6","key":"8314_CR15","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1016\/j.cell.2015.02.029","volume":"160","author":"V Presnyak","year":"2015","unstructured":"Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, Coller J (2015) Codon optimality is a major determinant of mRNA stability. Cell 160(6):1111\u20131124. https:\/\/doi.org\/10.1016\/j.cell.2015.02.029","journal-title":"Cell"},{"issue":"6164","key":"8314_CR16","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1126\/science.1243490","volume":"342","author":"AB Stergachis","year":"2013","unstructured":"Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342(6164):1367\u20131372. https:\/\/doi.org\/10.1126\/science.1243490","journal-title":"Science"},{"issue":"suppl2","key":"8314_CR17","doi-asserted-by":"publisher","first-page":"W132","DOI":"10.1093\/nar\/gkm392","volume":"35","author":"MC Angellotti","year":"2007","unstructured":"Angellotti MC, Bhuiyan SB, Chen G, Wan XF (2007) CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Res 35(suppl2):W132\u2013W136. https:\/\/doi.org\/10.1093\/nar\/gkm392","journal-title":"Nucleic Acids Res"},{"key":"8314_CR18","doi-asserted-by":"publisher","unstructured":"Dixit R, Kumar A, Mohapatra B (2019) Implication of GATA4 synonymous variants in congenital heart disease: a comprehensive in-silico approach. Mutat Research\/Fundamental Mol Mech Mutagen 813. https:\/\/doi.org\/10.1016\/j.mrfmmm.2018.12.002. :31 \u2013 8","DOI":"10.1016\/j.mrfmmm.2018.12.002"},{"key":"8314_CR19","doi-asserted-by":"publisher","first-page":"111741","DOI":"10.1016\/j.mrfmmm.2021.111741","volume":"822","author":"ML Yadav","year":"2021","unstructured":"Yadav ML, Jain D, Agrawal D, Kumar A, Mohapatra B (2021) A gain-of-function mutation in CITED2 is associated with congenital heart disease. Mutat Research\/Fundamental Mol Mech Mutagen 822:111741. https:\/\/doi.org\/10.1016\/j.mrfmmm.2021.111741","journal-title":"Mutat Research\/Fundamental Mol Mech Mutagen"},{"key":"8314_CR20","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature08909","volume":"463","author":"TW Nilsen","year":"2010","unstructured":"Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457\u2013463. https:\/\/doi.org\/10.1038\/nature08909","journal-title":"Nature"},{"issue":"1","key":"8314_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-018-1437-x","volume":"19","author":"SI Adamson","year":"2018","unstructured":"Adamson SI, Zhan L, Graveley BR (2018) Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency. Genome Biol 19(1):1\u20132. https:\/\/doi.org\/10.1186\/s13059-018-1437-x","journal-title":"Genome Biol"},{"issue":"suppl2","key":"8314_CR22","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gkh393","volume":"32","author":"WG Fairbrother","year":"2004","unstructured":"Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB (2004) RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 32(suppl2):W187\u2013W190. https:\/\/doi.org\/10.1093\/nar\/gkh393","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"8314_CR23","doi-asserted-by":"publisher","first-page":"3568","DOI":"10.1093\/nar\/gkg616","volume":"31","author":"L Cartegni","year":"2003","unstructured":"Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res 31(13):3568\u20133571. https:\/\/doi.org\/10.1093\/nar\/gkg616","journal-title":"Nucleic Acids Res"},{"key":"8314_CR24","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1101\/gad.1195304","volume":"18","author":"XH Zhang","year":"2004","unstructured":"Zhang XH, Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 18:1241\u20131250. https:\/\/doi.org\/10.1101\/gad.1195304","journal-title":"Genes Dev"},{"key":"8314_CR25","doi-asserted-by":"publisher","unstructured":"Zhang C, Li WH, Krainer AR, Zhang MQ (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc. Natl Acad. Sci. USA105:5797\u20135802. https:\/\/doi.org\/10.1073\/pnas.0801692105","DOI":"10.1073\/pnas.0801692105"},{"key":"8314_CR26","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.1093\/nar\/gkh341","volume":"32","author":"M Sironi","year":"2004","unstructured":"Sironi M, Menozzi G, Riva L, Cagliani R, Comi GP, Bresolin N, Giorda R, Pozzoli U (2004) Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Res 32:1783\u20131791. https:\/\/doi.org\/10.1093\/nar\/gkh341","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"8314_CR27","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/0092-8674(94)90192-9","volume":"79","author":"S Arber","year":"1994","unstructured":"Arber S, Halder G, Caroni P (1994) Muscle LIM protein, a novel essential regulator of myogenesis, promotes myogenic differentiation. Cell 79(2):221\u2013231. https:\/\/doi.org\/10.1016\/0092-8674(94)90192-9","journal-title":"Cell"},{"issue":"2","key":"8314_CR28","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1007\/s00441-004-0873-y","volume":"317","author":"K Gehmlich","year":"2004","unstructured":"Gehmlich K, Geier C, Osterziel KJ, Van der Ven PF, F\u00fcrst DO (2004) Decreased interactions of mutant muscle LIM protein (MLP) with N-RAP and \u03b1-actinin and their implication for hypertrophic cardiomyopathy. Cell Tissue Res 317(2):129\u2013136. https:\/\/doi.org\/10.1007\/s00441-004-0873-y","journal-title":"Cell Tissue Res"},{"issue":"1\u20132","key":"8314_CR29","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/S1096-7192(03)00142-2","volume":"80","author":"B Mohapatra","year":"2003","unstructured":"Mohapatra B, Jimenez S, Lin JH, Bowles KR, Coveler KJ, Marx JG, Chrisco MA, Murphy RT, Lurie PR, Schwartz RJ, Elliott PM (2003) Mutations in the muscle LIM protein and \u03b1-actinin-2 genes in dilated cardiomyopathy and endocardialfibroelastosis. Mol Genet Metab 80(1\u20132):207\u2013215. https:\/\/doi.org\/10.1016\/S1096-7192(03)00142-2","journal-title":"Mol Genet Metab"},{"issue":"1","key":"8314_CR30","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.ymgme.2005.10.008","volume":"88","author":"JM Bos","year":"2006","unstructured":"Bos JM, Poley RN, Ny M, Tester DJ, Xu X, Vatta M, Towbin JA, Gersh BJ, Ommen SR, Ackerman MJ (2006) Genotype\u2013phenotype relationships involving hypertrophic cardiomyopathy-associated mutations in titin, muscle LIM protein, and telethonin. Mol Genet Metab 88(1):78\u201385. https:\/\/doi.org\/10.1016\/j.ymgme.2005.10.008","journal-title":"Mol Genet Metab"},{"issue":"5","key":"8314_CR31","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1097\/GIM.0b013e3181d6f7c0","volume":"12","author":"RS Zimmerman","year":"2010","unstructured":"Zimmerman RS, Cox S, Lakdawala NK, Cirino A, Mancini-DiNardo D, Clark E, Leon A, Duffy E, White E, Baxter S, Alaamery M (2010) A novel custom resequencing array for dilated cardiomyopathy. Genet Sci 12(5):268\u2013278. https:\/\/doi.org\/10.1097\/GIM.0b013e3181d6f7c0","journal-title":"Genet Sci"},{"key":"8314_CR32","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.gene.2018.07.036","volume":"676","author":"A Janin","year":"2018","unstructured":"Janin A, Bessi\u00e8re F, Chauveau S, Chevalier P, Millat G (2018) First identification of homozygous truncating CSRP3 variants in two unrelated cases with hypertrophic cardiomyopathy. Gene 676:110\u2013116. https:\/\/doi.org\/10.1016\/j.gene.2018.07.036","journal-title":"Gene"},{"issue":"2","key":"8314_CR33","doi-asserted-by":"publisher","first-page":"89","DOI":"10.20452\/pamw.15130","volume":"130","author":"M Lipari","year":"2020","unstructured":"Lipari M, Wypasek E, Karpi\u0144ski M, Tomkiewicz-Pajak L, Laino L, Binni F, Giannarelli D, Rubi\u015b P, Petkow-Dimitrow P, Undas A, Grammatico P (2020) Identification of a variant hotspot in MYBPC3 and of a novel CSRP3 autosomal recessive alteration in a cohort of polish patients with hypertrophic cardiomyopathy. Pol archives Intern Med 130(2):89\u201399. https:\/\/doi.org\/10.20452\/pamw.15130","journal-title":"Pol archives Intern Med"},{"issue":"5","key":"8314_CR34","doi-asserted-by":"publisher","first-page":"442","DOI":"10.15252\/emmm.201506055","volume":"8","author":"S Diederichs","year":"2016","unstructured":"Diederichs S, Bartsch L, Berkmann JC, Fr\u00f6se K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T (2016) The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 8(5):442\u2013457. https:\/\/doi.org\/10.15252\/emmm.201506055","journal-title":"EMBO Mol Med"},{"issue":"12","key":"8314_CR35","doi-asserted-by":"publisher","first-page":"1914","DOI":"10.1093\/bioinformatics\/btw086","volume":"32","author":"P Wen","year":"2016","unstructured":"Wen P, Xiao P, Xia J (2016) dbDSM: a manually curated database for deleterious synonymous mutations. Bioinformatics 32(12):1914\u20131916. https:\/\/doi.org\/10.1093\/bioinformatics\/btw086","journal-title":"Bioinformatics"},{"issue":"10","key":"8314_CR36","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1038\/nrg3051","volume":"12","author":"ZE Sauna","year":"2011","unstructured":"Sauna ZE, Kimchi-Sarfaty C (2011) Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 12(10):683\u2013691. https:\/\/doi.org\/10.1038\/nrg3051","journal-title":"Nat Rev Genet"},{"issue":"6","key":"8314_CR37","doi-asserted-by":"publisher","first-page":"1324","DOI":"10.1016\/j.cell.2014.01.051","volume":"156","author":"F Supek","year":"2014","unstructured":"Supek F, Mi\u00f1ana B, Valc\u00e1rcel J, Gabald\u00f3n T, Lehner B (2014) Synonymous mutations frequently act as driver mutations in human cancers. Cell 156(6):1324\u20131335. https:\/\/doi.org\/10.1016\/j.cell.2014.01.051","journal-title":"Cell"},{"issue":"7","key":"8314_CR38","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1016\/j.tig.2014.04.006","volume":"30","author":"RC Hunt","year":"2014","unstructured":"Hunt RC, Simhadri VL, Iandoli M, Sauna ZE, Kimchi-Sarfaty C (2014) Exposing synonymous mutations. Trends Genet 30(7):308\u2013321. https:\/\/doi.org\/10.1016\/j.tig.2014.04.006","journal-title":"Trends Genet"},{"issue":"3","key":"8314_CR39","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/j.jmb.2012.06.010","volume":"422","author":"PS Spencer","year":"2012","unstructured":"Spencer PS, Siller E, Anderson JF, Barral JM (2012) Silent substitutions predictably alter translation elongation rates and protein folding efficiencies. J Mol Biol 422(3):328\u2013335. https:\/\/doi.org\/10.1016\/j.jmb.2012.06.010","journal-title":"J Mol Biol"},{"issue":"6","key":"8314_CR40","doi-asserted-by":"publisher","first-page":"e38864","DOI":"10.1371\/journal.pone.0038864","volume":"7","author":"NC Edwards","year":"2012","unstructured":"Edwards NC, Hing ZA, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CE, Shapiro A, Okunji C (2012) Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches. PLoS ONE 7(6):e38864. https:\/\/doi.org\/10.1371\/journal.pone.0038864","journal-title":"PLoS ONE"},{"issue":"31","key":"8314_CR41","doi-asserted-by":"publisher","first-page":"12120","DOI":"10.1074\/jbc.RA118.001805","volume":"293","author":"AC Bertalovitz","year":"2018","unstructured":"Bertalovitz AC, Badhey ML, McDonald TV (2018) Synonymous nucleotide modification of the KCNH2 gene affects both mRNA characteristics and translation of the encoded hERG ion channel. J Biol Chem 293(31):12120\u201312136. https:\/\/doi.org\/10.1074\/jbc.RA118.001805","journal-title":"J Biol Chem"},{"issue":"1","key":"8314_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-019-10489-2","volume":"10","author":"Y Sharma","year":"2019","unstructured":"Sharma Y, Miladi M, Dukare S, Boulay K, Caudron-Herger M, Gro\u00df M, Backofen R, Diederichs S (2019) A pan-cancer analysis of synonymous mutations. Nat Commun 10(1):1\u20134. https:\/\/doi.org\/10.1038\/s41467-019-10489-2","journal-title":"Nat Commun"},{"issue":"6","key":"8314_CR43","doi-asserted-by":"publisher","first-page":"e73","DOI":"10.1093\/nar\/gks1473","volume":"41","author":"P Gaspar","year":"2013","unstructured":"Gaspar P, Moura G, Santos MA, Oliveira JL (2013) mRNA secondary structure optimization using a correlated stem\u2013loop prediction. Nucleic Acids Res 41(6):e73\u2013e73","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"8314_CR44","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1006\/jmbi.1994.1714","volume":"244","author":"MH de Smit","year":"1994","unstructured":"de Smit MH, van Duin J (1994) Control of translation by mRNA secondary structure in Escherichia coli: a quantitative analysis of literature data. J Mol Biol 244(2):144\u2013150","journal-title":"J Mol Biol"},{"issue":"5850","key":"8314_CR45","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1038\/295616a0","volume":"295","author":"MN Hall","year":"1982","unstructured":"Hall MN, Gabay J, D\u00e9barbouill\u00e9 M, Schwartz M (1982) A role for mRNA secondary structure in the control of translation initiation. Nature 295(5850):616\u2013618","journal-title":"Nature"},{"key":"8314_CR46","doi-asserted-by":"crossref","unstructured":"Kozak M (1986) Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proceedings of the National Academy of Sciences, 83(9), 2850\u20132854","DOI":"10.1073\/pnas.83.9.2850"},{"issue":"1","key":"8314_CR47","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.molcel.2006.02.014","volume":"22","author":"SM Studer","year":"2006","unstructured":"Studer SM, Joseph S (2006) Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell 22(1):105\u2013115","journal-title":"Mol Cell"},{"issue":"22","key":"8314_CR48","doi-asserted-by":"publisher","first-page":"10898","DOI":"10.1093\/nar\/gkw671","volume":"44","author":"G Faure","year":"2016","unstructured":"Faure G, Ogurtsov AY, Shabalina SA, Koonin EV (2016) Role of mRNA structure in the control of protein folding. Nucleic Acids Res 44(22):10898\u201310911","journal-title":"Nucleic Acids Res"},{"key":"8314_CR49","doi-asserted-by":"crossref","unstructured":"Wen, J. D., Lancaster, L., Hodges, C., Zeri, A. C., Yoshimura, S. H., Noller, H. F.,\u2026 Tinoco, I. (2008). Following translation by single ribosomes one codon at a time.Nature, 452(7187), 598\u2013603","DOI":"10.1038\/nature06716"},{"issue":"6","key":"8314_CR50","doi-asserted-by":"publisher","first-page":"2367","DOI":"10.1093\/nar\/gkq1118","volume":"39","author":"N Locker","year":"2011","unstructured":"Locker N, Chamond N, Sargueil B (2011) A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3. Nucleic Acids Res 39(6):2367\u20132377","journal-title":"Nucleic Acids Res"},{"key":"8314_CR51","doi-asserted-by":"crossref","unstructured":"Watts, J. M., Dang, K. K., Gorelick, R. J., Leonard, C. W., Bess Jr, J. W., Swanstrom,R., \u2026 Weeks, K. M. (2009). Architecture and secondary structure of an entire HIV-1 RNA genome. Nature, 460(7256), 711\u2013716","DOI":"10.1038\/nature08237"},{"issue":"5811","key":"8314_CR52","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1126\/science.1135308","volume":"315","author":"C Kimchi-Sarfaty","year":"2007","unstructured":"Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007) A\u201d silent\u201d polymorphism in the MDR 1 gene changes substrate specificity. Science 315(5811):525\u2013528","journal-title":"Science"},{"key":"8314_CR53","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1007\/978-3-319-23476-2_6","volume-title":"ABC Transporters-40 years on","author":"KL Fung","year":"2016","unstructured":"Fung KL, Hunt RC, Kimchi-Sarfaty C, Gottesman MM (2016) Genetic polymorphisms of P-glycoprotein: echoes of silence. ABC Transporters-40 years on. Springer, Cham, pp 105\u2013134"},{"key":"8314_CR54","doi-asserted-by":"crossref","unstructured":"Bartoszewski, R. A., Jablonsky, M., Bartoszewska, S., Stevenson, L., Dai, Q., Kappes,J., \u2026 Bebok, Z. (2010). A synonymous single nucleotide polymorphism in \u2206F508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein. Journal of Biological Chemistry, 285(37), 28741\u201328748","DOI":"10.1074\/jbc.M110.154575"},{"issue":"2","key":"8314_CR55","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.nbd.2006.03.007","volume":"23","author":"WW Ge","year":"2006","unstructured":"Ge WW, Leystra-Lantz C, Sanelli TR, McLean J, Wen W, Strong W, Strong MJ (2006) Neuronal tissue-specific ribonucleoprotein complex formation on SOD1 mRNA: alterations by ALS SOD1 mutations. Neurobiol Dis 23(2):342\u2013350","journal-title":"Neurobiol Dis"},{"issue":"4","key":"8314_CR56","doi-asserted-by":"publisher","first-page":"2073","DOI":"10.1093\/nar\/gks1205","volume":"41","author":"SA Shabalina","year":"2013","unstructured":"Shabalina SA, Spiridonov NA, Kashina A (2013) Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 41(4):2073\u20132094","journal-title":"Nucleic Acids Res"},{"issue":"5998","key":"8314_CR57","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1126\/science.1191701","volume":"329","author":"F Zhang","year":"2010","unstructured":"Zhang F, Saha S, Shabalina SA, Kashina A (2010) Differential arginylation of actin isoforms is regulated by coding sequence\u2013dependent degradation. Science 329(5998):1534\u20131537","journal-title":"Science"},{"key":"8314_CR58","doi-asserted-by":"crossref","unstructured":"Zhang, F., Patel, D. M., Colavita, K., Rodionova, I., Buckley, B., Scott, D. A., \u2026Kashina, A. (2015). Arginylation regulates purine nucleotide biosynthesis by enhancing the activity of phosphoribosyl pyrophosphate synthase. Nature communications, 6(1),1\u20139","DOI":"10.1038\/ncomms8517"},{"key":"8314_CR59","doi-asserted-by":"crossref","unstructured":"Shatoff E, Bundschuh R (2020) Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures.PLoS Computational Biology, 16(5), e1007852","DOI":"10.1371\/journal.pcbi.1007852"},{"key":"8314_CR60","doi-asserted-by":"publisher","unstructured":"Mauger DM, Cabral BJ, Presnyak V, Su SV, Reid DW, Goodman B, Link K, Khatwani N, Reynders J, Moore MJ, McFadyen IJ (2019) mRNA structure regulates protein expression through changes in functional half-life. Proceedings of the National Academy of Sciences 116(48):24075-83. https:\/\/doi.org\/10.1073\/pnas.1908052116","DOI":"10.1073\/pnas.1908052116"},{"issue":"7485","key":"8314_CR61","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/nature12756","volume":"505","author":"Y Ding","year":"2014","unstructured":"Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505(7485):696\u2013700. https:\/\/doi.org\/10.1038\/nature12756","journal-title":"Nature"},{"issue":"12","key":"8314_CR62","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1016\/j.tibs.2015.10.005","volume":"40","author":"KS Koutmou","year":"2015","unstructured":"Koutmou KS, Radhakrishnan A, Green R (2015) Synthesis at the speed of codons. Trends Biochem Sci 40(12):717\u2013718. https:\/\/doi.org\/10.1016\/j.tibs.2015.10.005","journal-title":"Trends Biochem Sci"},{"key":"8314_CR63","doi-asserted-by":"publisher","first-page":"57","DOI":"10.2147\/RRBC.S83483","volume":"6","author":"S Mitra","year":"2016","unstructured":"Mitra S, Ray SK, Banerjee R (2016) Synonymous codons influencing gene expression in organisms. Rese Rep Biochem 6:57\u201365. https:\/\/doi.org\/10.2147\/RRBC.S83483","journal-title":"Rese Rep Biochem"},{"issue":"1","key":"8314_CR64","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/nrg.2015.3","volume":"17","author":"MM Scotti","year":"2016","unstructured":"Scotti MM, Swanson MS (2016) RNA mis-splicing in disease. Nat Rev Genet 17(1):19\u201332. https:\/\/doi.org\/10.1038\/nrg.2015.3","journal-title":"Nat Rev Genet"},{"key":"8314_CR65","doi-asserted-by":"crossref","unstructured":"Ke S, Shang S, Kalachikov SM, Morozova I, Yu L, Russo JJ, \u2026 Chasin LA (2011) Quantitative evaluation of all hexamers as exonic splicing elements. Genome research 21(8):1360\u20131374 https:\/\/doi.org\/10.1101\/gr.119628.110","DOI":"10.1101\/gr.119628.110"},{"issue":"10","key":"8314_CR66","doi-asserted-by":"publisher","first-page":"5493","DOI":"10.1093\/nar\/gkac270","volume":"50","author":"RJ Pengelly","year":"2022","unstructured":"Pengelly RJ, Bakhtiar D, Borovsk\u00e1 I, Kr\u00e1lovi\u010dov\u00e1 J, Vo\u0159echovsk\u00fd I (2022) Exonic splicing code and protein binding sites for calcium. Nucleic Acids Res 50(10):5493\u20135512. https:\/\/doi.org\/10.1093\/nar\/gkac270","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"8314_CR67","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1161\/CIRCRESAHA.107.163147","volume":"101","author":"MV Latronico","year":"2007","unstructured":"Latronico MV, Catalucci D, Condorelli G (2007) Emerging role of microRNAs in cardiovascular biology. Circul Res 101(12):1225\u20131236. https:\/\/doi.org\/10.1161\/CIRCRESAHA.107.163147","journal-title":"Circul Res"},{"issue":"3","key":"8314_CR68","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/ng.762","volume":"43","author":"P Brest","year":"2011","unstructured":"Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, Mari B, Barbry P, Mosnier JF, H\u00e9buterne X, Harel-Bellan A (2011) A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn\u2019s disease. Nat Genet 43(3):242\u2013245. https:\/\/doi.org\/10.1038\/ng.762","journal-title":"Nat Genet"},{"issue":"4","key":"8314_CR69","doi-asserted-by":"publisher","first-page":"e0249406","DOI":"10.1371\/journal.pone.0249406","volume":"16","author":"MA Sousa","year":"2021","unstructured":"Sousa MA, de Athayde FR, Maldonado MB, Lima AO, Fortes MR, Lopes FL (2021) Single nucleotide polymorphisms affect miRNA target prediction in bovine. PLoS ONE 16(4):e0249406. https:\/\/doi.org\/10.1371\/journal.pone.0249406","journal-title":"PLoS ONE"}],"container-title":["Molecular Biology Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11033-023-08314-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11033-023-08314-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11033-023-08314-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T16:46:41Z","timestamp":1682700401000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11033-023-08314-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,6]]},"references-count":69,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5]]}},"alternative-id":["8314"],"URL":"https:\/\/doi.org\/10.1007\/s11033-023-08314-7","relation":{},"ISSN":["0301-4851","1573-4978"],"issn-type":[{"value":"0301-4851","type":"print"},{"value":"1573-4978","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,6]]},"assertion":[{"value":"12 October 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"On behalf of all the authors, the corresponding author states that there is no conflict of interest. All the authors have read the manuscript and approved the submission of current version of the manuscript.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflicts of Interest\/Competing interests"}},{"value":"Authors have no relevant financial or non-financial interests to disclose.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Financial and non-Financial interest"}},{"value":"The study was approved by the \u2018Institutional human ethics committee\u2019.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"All the study subjects gave prior written informed consent for collection of samples.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to participate"}}]}}