Naslov
Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ
(Computational analysis of MT retrotransposons in mouse strains C57BL/6J and PWK/PhJ)

Autori
Štancl, Paula

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, diplomski rad

Fakultet
Prirodoslovno-matematički fakultet

Mjesto
Zagreb

Datum
16.07

Godina
2020

Stranica
49

Mentor
Vlahoviček, Kristian

Neposredni voditelj
Kuzman, Maja

Ključne riječi
LTR retrotranspozoni ; sojevi miševa ; računalna genomika
(LTR retrotransposons ; mouse strains ; computational genomics)

Sažetak
Rodent-specific MT retrotransposons belong to a class of LTR retrotransposons. Full-length MT elements contain two long terminal repeats (LTRs) and an internal sequence. Due to ectopic recombination, the internal sequence of full- length MT elements is excised producing a solo LTR. The standard annotation of retrotransposons is done with RepeatMasker program which one of the major drawbacks is the precise annotation of full- length elements. The goal of this thesis was to improve the RepeatMasker annotation of MT elements and to identify homologous between a classical mouse strain C57BL/6J and a wild-derived mouse strain PWK/PhJ. The developed computational method focuses on the conserved length of their LTRs and has resulted in a larger number of annotated full- length MT elements in in the mouse strain C57BL/6J. Phylogenetically younger and still active annotated full-length MT elements, MTA and MTB, had more new C57BL/6J-strains specific elements that have emerged after the separations of the strains. On the other hand, older MT elements were more conserved among strains. Conserved and strain-specific MT element integrations into genes mostly occurred in introns of protein-coding genes. Identified new C57BL/6J- strains specific elements integrated into exons of olfactory receptor genes, may contribute to phenotypic differences between mouse strains C57BL/6J and PWK/PhJ.

Izvorni jezik
Engleski

Znanstvena područja
Biologija

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