PMID: 11912182Mar 26, 2002Paper

Classification of common conserved sequences in mammalian intergenic regions

Human Molecular Genetics
Alexey S Kondrashov, Svetlana A Shabalina

Abstract

Comparisons between orthologous intergenic regions of related genomes reveal numerous hits, i.e. pairs of relatively short highly similar sequences that evolved slowly, perhaps due to selective constraint. We analyzed and classified 2638 hits found within 100 pairs of complete, orthologous intergenic regions of human and murine genomes. We identified all common fragments of hits that align well with many other hits and constructed their classification. Our analysis revealed 20 abundant classes each containing 10 or more fragments. Fragments of the same class may perform the same function, e.g. bind a particular protein. Ten of the abundant classes apparently correspond to known functional consensuses, whereas others may represent novel conserved sites. Thus, large-scale comparative analysis of slowly evolving intergenic sequences can provide valuable insights into their function.

Citations

Feb 4, 2005·Journal of Genetics·Michael W Nachman
Mar 25, 2010·Genome Biology and Evolution·Liliana LosadaWilliam C Nierman
Nov 11, 2011·Genome Biology and Evolution·David ManagadzeEugene V Koonin
Dec 24, 2008·Human Molecular Genetics·Svetlana A ShabalinaLuda Diatchenko
Sep 5, 2003·Nucleic Acids Research·Svetlana A ShabalinaAlexey S Kondrashov
Jan 8, 2013·Nucleic Acids Research·Svetlana A ShabalinaAnna Kashina
Apr 18, 2009·BMC Genomics·Alissa M ReschEugene V Koonin
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Jul 5, 2005·Human Molecular Genetics·Gregory V KryukovShamil Sunyaev
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