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Let \\(\\mathcal{M}\\) denote the morphism category of finitely generated \\(R\\)-modules, and let \\(\\mathcal{S}\\) be the full subcategory of \\(\\mathcal{M}\\) consisting of monomorphisms, known as the submodule category. It is evident that  \\(\\mathcal{M}\\) is an abelian category and \\(\\mathcal{S}\\) is an additive subcategory of \\(\\mathcal{M}\\) which is closed under extensions. This article reveals that the Auslander transpose in the category \\(\\mathcal{S}\\) can be described explicitly within mod \\( R\\), the category of finitely generated \\(R\\)-modules. This result is exploited to study the linkage theory as well as the Auslander-Reiten theory in \\(\\mathcal{S}\\). In addition, motivated by a result of \\textit{C. M. Ringel} and \\textit{M. Schmidmeier} [Trans. Am. Math. Soc. 360, No. 2, 691--716 (2008; Zbl 1154.16011)], the authors show that the Auslander-Reiten translations in the subcategories \\(\\mathcal{H}\\) and \\(\\mathcal{G}\\), consisting of all morphisms which are maximal Cohen-Macaulay \\(R\\)-modules and Gorenstein projective morphisms, respectively, may be computed within mod \\(R\\) via \\(\\mathcal{G}\\)-covers. 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