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First published online 15 April 2003
doi: 10.1242/jcs.00444

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Genes coding for intermediate filament proteins: common features and unexpected differences in the genomes of humans and the teleost fish Fugu rubripes

¹ Max Planck Institute for Biophysical Chemistry, Department of Biochemistry, Am Fassberg 11, D-37077 Goettingen, Germany
² Department of Cell Biology, University of Bremen, Leobener Strasse NW II, D-28359 Bremen, Germany

View larger version (20K): [in a new window]   Fig. 1. F. rubripes scaffolds with two or three keratin genes and the collection of single keratin scaffolds. Scaffolds (Sc), given by number and size, and the areas occupied by the genes are from Table 1. Scaffolds are not drawn to scale. Keratin I and II genes are marked in red and green, respectively. Incomplete genes are marked by an indentation of the colored bars. Notice that four type II genes map next to type I genes, whereas the other two type II genes lie on scaffolds 285 and 3830. Thus, a keratin II gene cluster as in the human genome seems excluded. Also, 13 type I genes occur on seven scaffolds and the other six type I genes lie as single keratin I genes on other scaffolds (Table 1). Although the final view of keratin I gene mapping requires the full F. rubripes genome sequence, current results exclude the pure type I cluster present in the human genome. Other genes present on the scaffolds are given as uncolored boxes. Those with a human counterpart carry the corresponding accession number (Aparicio et al., 2002). These read, from top to bottom: X55733, initiation factor 4B; AB028998, tensin 2; NM_003056, solute carrier family (folate transporter), member 1; AF006085, ARP 2/3 complex subunit 2; M95627, angio-associated migratory cell protein AAMP; AF201422, splicing coactivator subunit SRM300; NM_007153, zinc finger protein 208; AF035262, BAF57; L08176, Epstein-Barr-virus-induced G-protein-coupled receptor; NM_032865, tensin-like protein fragment; AL033533, prostaglandin endoperoxide synthase 2; AB031041, LIM-homodomain protein 6.1a; AAK57478, elongation factor 1A binding protein; AF304450, sarcolemma asociated protein 1; AF298548, caspase recruitment domain protein 7; AAF53869, Drosophila CG13969-PA; 060628, transmembrane 4 superfamily, member 8; J03040, human SPAPC/osteonectin/BM-40; NP_683687, aprataxin, novel nuclear protein; J03537, ribosomal protein S6; L14812, retinoblastoma related protein p107; XP_203519, murine Mycbp-associated protein. Unnamed boxes indicate hypothetical genes.

View larger version (87K): [in a new window]   Fig. 2. Examples of pairwise sequence comparisons of F. rubripes (F) and human (H) type I to IV proteins. (a) A F. rubripes keratin I (scaffold 3159) and human keratin 18. (b) A F. rubripes keratin II (scaffold 3159) and human keratin 8. (c) F. rubripes desmin 1 (scaffold 138) and human desmin (type III). (d) F. rubripes and human -internexin; the F. rubripes protein is from scaffold 1912 (Table 1). Identical amino acid residues in each pair are marked by bold print.

View larger version (15K): [in a new window]   Fig. 3. Schematic diagram of the location of introns in human (h) and F. rubripes (F) type I-IV genes. Only introns related to the region encoding the central rod domains (sketch of coils 1a, 1b and 2 at the top) are shown. Notice the related but not identical intron patterns of type I, II and III genes (red triangles), which are shared by human and F. rubripes, and the entirely different intron pattern of type IV genes (blue triangles). All seven human type IV genes show the two conserved intron positions, and the NF-H gene has an additional third intron (open triangle) marked by a vertical line. This pattern holds in F. rubripes for six genes (gefiltin, gefiltin like-2, NF-L-like 1, NF-M, NF-H-like and Y), with NF-H resembling human NF-H by the additional intron (open triangle marked by a vertical line). The other three F. rubripes type IV genes have either one (NF-L-like 2; third line from bottom) or two (gefiltin-like-1; second line from bottom) novel intron positions (black triangles); F. rubripes gene X (bottom line) has the two type IV intron positions (blue) and three type I to III intron positions (red) together with three novel intron positions (black).

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