Protein domains (center) show good correspondence with exon boundaries of HLA-DPB1 Expression and Its Relation to Structural Mismatch Models in. of correspondences between exons and units of protein structure-function that relationship of exons to protein structure represents a degenerate state of an. Several studies on exon shuffling on the correlation of exons with structural.
Alternative transcription and two modes of splicing results in two myosin light chains from one gene. Two Drosophila melanogaster tropomyosin genes: The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family. Molecular structure of the human cytoplasmic beta-actin gene: Structure of a human smooth muscle actin gene aortic type with a unique intron site. Complete structure of the alpha B-crystallin gene: Structure of the mouse glial fibrillary acidic protein gene: Structure of a gene for the human epidermal kDa keratin.
Structure of mouse kallikrein gene family suggests a role in specific processing of biologically active peptides. The sequences of an expressed rat alpha-tubulin gene and a pseudogene with an inserted repetitive element. Structural features and restricted expression of a human alpha-tubulin gene. Coding sequence and growth regulation of the human vimentin gene.
Do exons code for structural or functional units in proteins?
Sequence analysis of the human major histocompatibility gene SX alpha. Primary structure of the gene encoding rat preprosomatostatin. Gene structure of human cardiac hormone precursor, pronatriodilatin. The structure and evolution of the two nonallelic rat preproinsulin genes. Primary structure and evolution of rat growth hormone gene.
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Characterization of the structural gene and putative 5'-regulatory sequences for human proopiomelanocortin. Genomic organization of rat prolactin and growth hormone genes. Cloning and expression of the rat interleukin-3 gene. Genetic organization of the c-sis transcription unit.
Structural organization and nucleotide sequence of mouse c-myb oncogene: Sequence and organization of genes encoding the human 27 kDa heat shock protein. Structure of the human oestrogen-responsive gene pS2. Structure, expression, and chromosomal location of the human c-fgr gene. Characterization of the human p53 gene.
Structure of the two related elastase genes expressed in the rat pancreas.
Exon–domain correlation and its corollaries | Bioinformatics | Oxford Academic
Intron-exon splice junctions map at protein surfaces. Isolation and sequence of a rat chymotrypsin B gene. Genetic engineering in the Precambrian: The triosephosphate isomerase gene from maize: Gene organization of the small subunit of human calcium-activated neutral protease. Protein structure and gene organization of mouse lactate dehydrogenase-A isozyme.
Do exons code for structural or functional units in proteins?
Intron-dependent evolution of chicken glyceraldehyde phosphate dehydrogenase gene. Complete sequence of the chicken glyceraldehydephosphate dehydrogenase gene. Primary structure of the mouse glycerolphosphate dehydrogenase gene. Intron-dependent evolution of the nucleotide-binding domains within alcohol dehydrogenase and related enzymes.mRNA Splicing
Correlation of exons with structural domains in alcohol dehydrogenase. Evolution of aspartyl proteases by gene duplication: Structure of the human phosphoglycerate kinase gene and the intron-mediated evolution and dispersal of the nucleotide-binding domain.
Organization of the gene encoding the human beta-hexosaminidase alpha-chain. Intragenic amplification and divergence in the mouse alpha-fetoprotein gene. The structural organization of the chicken calmodulin gene. A gene encoding rat cholecystokinin. Isolation, nucleotide sequence, and promoter activity.
Four of six exons encode separate functional domains of rat pre-proglucagon. Human epidermal growth factor precursor: Gene encoding parathyroid hormone.
Nucleotide sequence of the rat gene and deduced amino acid sequence of rat preproparathyroid hormone. Alternative splicing accounts for the four forms of myelin basic protein. Individual exons encode the integral membrane domains of human myelin proteolipid protein.
Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin. A pseudogene homologous to mouse transplantation antigens: Cloning and sequence analysis of calf cDNA and human genomic DNA encoding alpha-subunit precursor of muscle acetylcholine receptor. Structure linkage, and sequence of the two genes encoding the delta and gamma subunits of the nicotinic acetylcholine receptor.
The LDL receptor gene: Gene and protein structure of a beta-crystallin polypeptide in murine lens: Isolation and characterization of overlapping genomic clones covering the chicken alpha 2 type I collagen gene. Graph representation of such networks abstracts them as nodes connected by edges e. Network properties are mainly analyzed from the prospective of their node connectivity or degree distribution.
Thus there are many poorly connected nodes and very few hubs in such networks. Earlier, we have shown Liu et al. Exon-bordering domains also co-occur with a larger number of different domains to form mosaic proteins with diverse domain architectures.
This property suggests that exon-bordering domains should be found among the highly connected hubs and that the evolution of domain networks at least in terms of degree distribution is likely to be largely driven by the evolution of exon-bordering domains and their propagation into genes via exon shuffling and duplication mechanisms.
Indeed, many properties of the network of co-occurring protein domains, where each domains in human is a node and an edge represents co-occurrence of two domains not necessarily adjacent in one protein, are similar to other biological networks described. We found that this undirected network is also scale-free [data not shown, this result is analogous to already published reports Apic et al. Thus, most of the domain pairs can be found only in one protein per pair.
Such proteins, however, are often domain-rich. We also calculated the expected distribution of co-occurring pairs by modeling domain co-occurrence as a Bernoulli process where a pair frequency would be proportional to the product of frequencies of individual domains, derived in this case from the number of proteins containing a domain, rather than domain numbers.
Similar findings obtained by other methods have been very recently published for the domain families in SCOP Vogel et al. As a group, exon-bordering domains show a much higher connectivity Fig. We analyzed the level of network fragmentation after the removal of mobile domains by calculating the number of components, or remaining connected subgraphs, and average degree. We also estimated the distributions of these parameters for networks obtained from the network we studied by removal of the corresponding number of random nodes.
Removal of mobile domains results in substantial fragmentation of the network and a drop in the average degree, significantly different from random node removals Fig. Thus, mobile domains appear to be the major determinants of the network topology and evolution. For computational prediction of protein domains in human proteins retrieved from the Ensembl Birney et al.
We collected statistics for only one multi-exon transcript per gene whose protein translation had at least one domain.
Remarkably, when we detected correlation of the borders of protein domains with encoding exons, it was nearly always positive, i. However, there was one notable exception: This was rather surprising since the immunoglobulin domain was considered to be mobile and its bounding introns to have phase 1—1, which is the characteristic of mobile domains Kolkman and Stemmer, Upon further investigation, we noticed that the Pfam definition of Ig domain was actually 8—20 amino acids shorter than its counterpart domain definition from the SMART database.
Owing to this reason, the amino acid positions immediately outside the Ig domain border boxes as defined by Pfam were actually right inside the domain border boxes as defined by SMART.
This indicates a preference for the SMART domain definition because we consistently observed lower numbers of exon borders inside Pfam-specific Ig domain border boxes Fig. When we switched to using SMART domain definition for Ig domains, we discovered that the two most prevalent Ig-related domains in SMART, IGc1 and IG, were ranked 2 and 7, respectively, out of all human mobile domains, with both having positive correlation with exons in contrast to the results obtained from Pfam's Ig domain definition.
This contrast is even more obvious on the correlation graph for these domains Fig. IGc1 also has a strong positive correlation peak outside the domain, while Pfam's Ig domain showed a negative correlation with exon border at every position in the domain border box, both inside and outside of the domain borders. In addition, if we separate statistics collected from the domain border boxes at the start and at the end of domains, we could produce a correlation graph that gives us information on where the exon borders preferentially fall at the start and end of domains data not shown.
Our study identified FA58C as a mobile domain that correlates with multiple exons and displays a very strong preference for phase 1—1 introns.