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provided online are uniquely identified by clone name and extension, e.g., K08C7.3
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Sequences in the Wormpep database (release 17), provided online at www.sanger.ac.uk/Projects/C_elegans/ wormpep/, are uniquely identified by clone name and extension, e.g., K08C7.3.
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Sequences in the Wormpep Database (Release 17)
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12
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0343847392
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note
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Nematode-specific motifs: DC, SX (SXC), CT, VE, FE, CX, DB, EA, IY (worm_family_2), CZ, T4 (worm_ family_8), CN, EB, DD, MC, MD, DX, ES, and ET.
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13
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0343411381
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Supplementary material in the form of a table and expanded figures 1 and 2 is available to Science Online subscribers
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Supplementary material in the form of a table and expanded figures 1 and 2 is available to Science Online subscribers at www.scienceonline/feature/ data/1036101.shl
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14
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0342976069
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note
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2-terminus; NL, Notch/LIN-12; PD, P-type/trefoil; PX, plexin; SE, SEA; SM, semaphorin; SR, scavenger receptor C-rich; T1, thrombospondin 1; TY, thyroglobulin I; UL, sea urchin egg lectin; VC, von Willebrand factor C; VD, von Willebrand factor D; and WA, WAP (4-disulfide core). Note: the solidus is used to conform with the annotation system of Pfam.
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This EST sample has 40,379 clones representing 40% (7432) of the predicted protein-coding genes in Wormpep
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Superfamilies comprise proteins with a specified region of homotogy, for example, proteins belong to the IG superfamily if they have one or more IG modules. Families comprise proteins with more-or-less identical domain organization, for example, the Notch family.
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Conservatively, CK (Pfam: cys_knot), FC (Pfam: F5_F8_type_c), FS (Pfam: Kazal), KR (Pfam: kringle), SR (Pfam: SRCR), and VD (Pfam: vwd) modules occur in at least 6, 13, 6, 5, 7, and 7 distinct structural contexts, respectively, among known vertebrate proteins.
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46
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0342541775
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Conceivably, some protein modules have been lost in particular lineages (discussed below); however, differential loss without any invention cannot satisfactorily account for the observed distribution of protein families and superfamilies among species.
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In the M176.8 (chitinase) family, 25 genes or pseudogenes are clustered at two sites on chromosome II intermixed with seven members of the kin-15 family (Fig. 3). Another 11 chitinase genes are found, singly or as tandem pairs, at nine separate sites throughout the genome. In the C01B7.7 family, 64 genes or pseudogenes are spread along chromosome V at 14 separate sites; 4 sites contain single genes, 9 sites contain 2 to 5 genes, and 1 site contains 29 genes of this family intermixed with at least seven other, locally duplicated gene families, in the interval from C50H11 to T20D4 (ca. 350 kbp). Another 12 genes in the C01B7.7 family are found at 7 separate sites on other chromosomes, including one site with 4 genes.
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Excluding loci identified using reverse genetics and let genes identified using regional balancers, the fraction of protein genes on each chromosome with known visible mutations falls from 6.4% (161/2508), 6.0% (167/ 2803), 5.5% (146/2631), 4.1% (133/3259), 4.0% (124/ 3094) to 3.0% (124/4082), as the proportions of genes on these chromosomes that are duplicated rises from 0.32, 0.31, 0.36, 0.39, 0.45 to 0.51, for chromosomes III, I, X, II, IV, and V, respectively.
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In a survey of presumptive olfactory receptors, E. R. Troemel et al. [Cell 83, 207 (1995)] reported that about half of the genes sampled, whether isolated or clustered, had upstream sequences capable of driving transgene expression in specific chemosensory neurons. It is uncertain whether this reflects gene expression in situ or just latent potentials of these sequences.
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Modern bacteria have evidently lost this and other capacities for RNA metabolism important for RNA life or the transition from RNA to DNA life.
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Further information is online at www.mpimf-heidelberg. mpg.de/ewgdn/genome_paper/.
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note
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We wish to thank C. Bargmann, R. Barstead, T: Cebula, C. Dunn, E. Kipreos, D. Moerman, S. Nowak, G. Ruvkun, and W. Wadsworth for helpful discussions. H.H. received fellowships from the Deutsche Forschungsgemeinschaft and Max-Planck-Gesellschaft. This paper was supported by a grant from the NIH and originally submitted 7 October 1998.
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