{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T03:14:02Z","timestamp":1788146042916,"version":"build-2803163510"},"reference-count":60,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"IDB RAS Government Basic Research Program","award":["0088-2024-0011"],"award-info":[{"award-number":["0088-2024-0011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: The 3\u2032 untranslated region (3\u2032 UTR) integrates cleavage and polyadenylation signals, microRNA targets, RNA-binding-protein sites, and RNA secondary structure, but the organizational levels that remain conserved during long-term sequence evolution are poorly understood. Methods: We analyzed the ras85D 3\u2032 UTR in 37 drosophilid taxa. Substitution rates were estimated by maximum likelihood and RelTime; insertions and deletions were reconstructed with ARPIP and summarized as insertion\u2013deletion evolutionary localizations (IELs). Mobile-element candidates were detected with CENSOR\/Repbase, and evolutionarily conserved motifs (ECMs) with MEME\/MAST. Functional and structural annotations were integrated for Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis and tested using permutation-based coverage, distance, boundary-neighborhood, and multilayer architecture analyses. Results: The 2247-column alignment yielded 959 block events (710 deletions and 249 insertions). Among 63 positive-length ingroup branches, 16 were deletion-enriched, three were insertion-enriched, and one showed bidirectional turnover. Thirty-four IELs projected to 27 D. melanogaster loci and were associated with ECMs. The final registry contained 390 primary functional objects and 1135 RNAfold-predicted structural segments. Predicted weakly conserved miRNA target sites were depleted in ECM_15 and ECM_11, whereas none of 12 Functional Distance tests was significant. APA objects were enriched near predicted structural-segment boundaries (O\/E = 5.21; FDR = 0.00761). SAME_MULTILOOP_INTERVAL showed reduced between-context variance (0.276\u00d7 null; FDR = 0.0233), and the DIFFERENT_MULTILOOP_ARMS \u2212 SAME_MULTILOOP_INTERVAL contrast was significant (p = 0.00149; FDR = 0.00447). Conclusions: The ras85D 3\u2032 UTR evolves as a mosaic system in which extensive deletion-biased sequence turnover coexists with conserved regulatory landmarks, recurrently remodeled local neighborhoods, and context-dependent structural\u2013functional architectures.<\/jats:p>","DOI":"10.3390\/genes17091041","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T02:08:58Z","timestamp":1788142138000},"page":"1041","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Evolutionary Plasticity, Conservation of Functional Motifs, and Structural\u2014Functional Architecture of the ras85D 3\u2032 UTR in Drosophila"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6179-6848","authenticated-orcid":false,"given":"Aleksey M.","family":"Kulikov","sequence":"first","affiliation":[{"name":"N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4873-0790","authenticated-orcid":false,"given":"Ekaterina A.","family":"Sivoplyas","sequence":"additional","affiliation":[{"name":"N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia"},{"name":"Campus of Biology and Chemistry, Department of Biochemistry, Molecular Biology, and Genetics, Moscow Pedagogical State University, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Oleg E.","family":"Lazebny","sequence":"additional","affiliation":[{"name":"N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Barrett, L.W., Fletcher, S., and Wilton, S.D. (2013). 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