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Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes.
- Source :
-
Genes . Jan2024, Vol. 15 Issue 1, p33. 14p. - Publication Year :
- 2024
-
Abstract
- The specific characteristics of k-mer words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 20734425
- Volume :
- 15
- Issue :
- 1
- Database :
- Academic Search Index
- Journal :
- Genes
- Publication Type :
- Academic Journal
- Accession number :
- 175078306
- Full Text :
- https://doi.org/10.3390/genes15010033