The difference from the control is that the TCM compounds interact with amino acids and become H-bonded in sequences 20 28 and 147 157, but not in sequences 90 98.
This lack of conservation is not a surprise because compensatory mutations occur widely in ncRNAs, and many ncRNAs are conserved in structure but not in sequence [ 42, 43].
Microsatellite alleles can generally be divided into two types: alleles that are identical in both length and sequence and those identical in length but not in sequence, the latter being known as homoplastic microsatellite alleles.
For instance, the 84-nucleotide (nt) long structure-anchored repression element (CAESAR) in CTGF[ 4] is highly conserved in structure but not in sequence, and is suspected to inhibit translation and affect mRNA stability [ 11].
Accordingly, one can divide microsatellite homoplasy into two types: (1) microsatellite alleles identical in length, but not in sequence (indistinguishable by fragment length analyses), and (2) alleles identical in both length and sequences, but with different evolutionary history (only detectable through mutations documented in known pedigrees).
We note that almost half of evolutionarily conserved non-coding gene-regulatory sequences in vertebrate genomes [ 35], and probably a similar fraction of those that are conserved in function and shape but not in sequence [ 36, 37], are located within this span of DNA adjoining transcription start sites of genes.
The latter gene, located between YJR107W and YJR108W, contains a frameshift in the 'reference' S. cerevisiae genome sequence of strain S288c, but not in alternative sequences of S288c obtained by Liti et al [ 22] and Miura et al [ 16], nor in sequences from other S. cerevisiae strains.
In this study, we demonstrated that JHN contained an allele of Pi7 in IRBL7-M sharing limited sequence differences in nucleotide but not in protein sequence.
If, for one or a few clones, additional substitutions are found present in the sequence of one PCR but not in the sequence of another PCR from the same sample, it is reasonable to attribute them to DNA damage, and thus they were not considered in the analyses.
All nucleotide changes were observed in virus sequences of palm civets from the market, but not in virus sequences of animal isolates from the restaurant.
We have identified one gene, MOGAT2 (ENSSSCG00000014861), with seven SNPs, of which four are present in Mangalicas, but not in other 56 sequenced pig individuals (see Results).
