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For example, B2 is comprised of a cluster of four smaller conserved regions.
To detect smaller conserved syntenies, we retained maximally 3000 alignments at each ancestral node, increased the gene coverage parameter to 4 and lowered the alignment score threshold to 1.
In addition, the presence of smaller, conserved orthology clusters of BTB/POZ and BTB/C-terminal Kelch proteins suggests that these likely target endogenous proteins, possibly for degradation in an E3 ligase proteolysis pathway (Petroski and Deshaies 2005).
Smaller conserved eukaryotic clusters included a number of proteins involved in vesicle transport, such as a Rab6 GTPase-activating protein involved in retrograde transport [ 67], the golgin CASP [ 68] and the vesicular transport proteins P115 (see Figure S3, additional file 2), autophagy protein APG6 [ 69, 70], and early endosome antigen (EEA1, [ 71]) homologs (see Figure S4, additional file 2).
genomes, is the main contributing factor explaining the Far04 smaller conserved core.
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MicroRNAs (miRNAs, miRs) are one class of small, conserved, single-stranded, noncoding RNA.
Three of the uniquely identified small protein candidates correspond to small conserved ORFs within the 5′ UTRs of larger genes.
We also observed six small, conserved families of ePK-related protein kinases, which are classified as other-ePKs [ 6] and five families of aPKs.
We exploit this property to avoid paralogous genes when creating paired sequences by restricting to gene pairs that have small, conserved intergenic distances.
Interestingly, the small, conserved exon 2 of var genes shows a different nucleosome enrichment pattern with the highest enrichment in schizonts, medium in rings and lowest in trophozoites.
Although there are a number of variations in deletion, insertion and rearrangement in each sequence, they consist of phage infection-related genes (e.g. NIES39_F00750) and small conserved putative genes, generating a direct repeat in some case.
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CEO of Professional Science Editing for Scientists @ prosciediting.com