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Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema

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Title Reverse Polarization in Amino acid and Nucleotide
Substitution Patterns Between Human–Mouse
Orthologs of Two Compositional Extrema
 
Creator Bag, Sumit K
Paul, Sandip
Ghosh, Subhagata
Dutta, Chitra
 
Subject Structural Biology & Bioinformatics
 
Description Genome-wide analysis of sequence divergence patterns in 12 024 human–mouse orthologous pairs reveals, for the
first time, that the trends in nucleotide and amino acid substitutions in orthologs of high and low GC composition
are highly asymmetric and polarized to opposite directions. The entire dataset has been divided into three groups
on the basis of the GC content at third codon sites of human genes: high, medium, and low. High-GC orthologs
exhibit significant bias in favor of the replacements, Thr ! Ala, Ser ! Ala, Val !Ala, Lys! Arg, Asn !Ser, Ile
! Val etc., from mouse to human, whereas in low-GC orthologs, the reverse trends prevail. In general, in the high-
GC group, residues encoded by A/U-rich codons of mouse proteins tend to be replaced by the residues encoded by
relatively G/C-rich codons in their human orthologs, whereas the opposite trend is observed among the low-GC orthologous
pairs. The medium-GC group shares some trends with high-GC group and some with low-GC group. The only
significant trend common in all groups of orthologs, irrespective of their GC bias, is (Asp)Mouse !(Glu)Human replacement.
At the nucleotide level, high-GC orthologs have undergone a large excess of (A/T)Mouse ! (G/C)Human substitutions
over (G/C)Mouse !(A/T)Human at each codon position, whereas for low-GC orthologs, the reverse is true.
Key words: high-GC orthologs; low-GC orthologs; amino acid replacement matrix; nucleotide replacement matrix;
sequence divergence
 
Date 2007
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/224/1/DNA_RESEARCH%2C14(_4)%2C141%2D154%2C2007[46].pdf
Bag, Sumit K and Paul, Sandip and Ghosh, Subhagata and Dutta, Chitra (2007) Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema. DNA Research, 14 (4). pp. 141-154.
 
Relation http://dx.doi.org/10.1093/dnares/dsm015
http://www.eprints.iicb.res.in/224/