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Exon-intron boundaries occur mostly in the loops connecting transmembrane segments [ 32] suggesting a modular gene structure reflecting the TMS-loop repeat units in SLC15A1.
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The plant genes and the animal genes each have modular gene structures with conserved intron positions.
In the case of At5g17165, the modular nature of the gene structure with the first exon encoding the targeting peptide is maintained.
We retrieved ENSEMBL gene structure information.
Evolutionary principles of modular gene regulation in yeasts.
SMART (Simple Modular Architecture Research Tool) functional domain searches located a conserved kinesin motor domain at the 5' end, with the 3' end likely conferring protein binding specificity (for discussion of kinesin gene structure, see [ 17]) [ 24].
These discrepancies can be explained by the structure of these modular genes, which share motifs in functional domains (e.g. HAMP, hemagglutinin, or autotransporter domains) and consequently have many sequence similarities.
We have recently shown that the method can be used to discover natural communities from social networks and to predict protein complexes from protein-protein interaction networks [ 28], while its effectiveness in finding intrinsic modular structures from gene expression data has not been thoroughly studied.
This part of the procedure is based on our method Modular Latent Structure Analysis (MLSA) [ 15], which searches for gene modules regulated by linear combinations of latent factors.
Overall, our results indicate that decomposition methods detect the modules which best correspond to the known modular structure within the gene regulatory network (Fig. 2a).
Although encoded by different genes, ERα and ERβ share the same general modular protein structure of the nuclear hormone receptor superfamily, and have almost 100% amino acid sequence homology in their DNA-binding domain.
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