Functionally significant features in the 5 ' untranslated region of the ABCA1 gene and their comparison in vertebrates

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F75010330%3A_____%2F19%3A00012660" target="_blank" >RIV/75010330:_____/19:00012660 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11140/19:10394875

Result on the web

<a href="https://www.mdpi.com/2073-4409/8/6/623" target="_blank" >https://www.mdpi.com/2073-4409/8/6/623</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/cells8060623" target="_blank" >10.3390/cells8060623</a>

Result language

angličtina

Original language name

Functionally significant features in the 5 ' untranslated region of the ABCA1 gene and their comparison in vertebrates

Original language description

Single nucleotide polymorphisms located in 5 ' untranslated regions (5 ' UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5 ' UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5 ' UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5 ' UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5 ' UTRs, such as GC content variation, hairpin structure conservation or 5 ' UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Cells

ISSN

2073-4409

e-ISSN

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Volume of the periodical

8

Issue of the periodical within the volume

6

Country of publishing house

CH - SWITZERLAND

Number of pages

24

Pages from-to

623

UT code for WoS article

000475309200111

EID of the result in the Scopus database

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