Common evolution of waprin and kunitz-like toxin families in Australian venomous snakes
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The conservation of alternative splicing in orthologous genes from the human and mouse genomes was analyzed. Alternatively spliced mouse genes from the AsMamDB database were used to scan the draft human genome. The mouse protein isoforms were aligned with respect to orthologous human genes, and thus the exon-intron structure of the latter was established. Proteins isoforms that could not be aligned throughout their length were analyzed in detail using the human EST alignment.
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T he inhibitors of NF‐κ B (Iκ B s) play an important role in the regulation of the NF‐κ B pathway. IκBR (for Iκ B ‐Related) is proposed to be a novel member of this family. We report the cloning and characterization of the region of the human gene encoding the previously reported mRNA. This region contains 13 exons, spread over 6550 bp of genomic sequence. The coding sequence is only weakly similar to other IκBs and the exons display a more complicated structure than has been found in other members of the IκB gene family. Moreover, the positions of intron‐exon junctions are different from those found in other IκB genes, even within the otherwise conserved ankyrin‐like repeat region, suggesting that the IκBR gene is not a member of this extended gene family. We report a revised mRNA and protein sequence for IκBR, which predicts that the protein is larger than originally described. We also report the chromosomal localisation of the human IκBR gene (approved gene symbol NFKBIL2 ) to 8q24.3 using PCR‐based somatic cell hybrid panel analysis and fluorescence in situ hybridization (FISH) mapping.
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A rabbit genomic clone containing the muscle phosphofructokinase (PFK) gene of approximately 17 kilobase pairs encoding 779 amino acids was isolated and sequenced. This gene contains 22 exons, ranging from 45 to 190 base pairs, and is split by 21 introns of 73-3500 base pairs. Eighty six percent of this gene is occupied by introns. An additional incomplete intron is found in the 5' flanking region, while an Alu-like sequence is identified in the 3' flanking region. The amino acid sequence translated from the coding sequence of this gene reveals 29 residues (amino acid numbers 479-507) which complete a previously unidentified gap Poorman, R. A. et al., Nature, 309, 467 (1984) and 4 positions of discrepancy; Ser (--->) Arg (268), Leu (--->) Pro (442), Ile (--->) Ser (558), and the insertion of an additional Arg at position 565. Twelve exons encoding the N-half of the protein are scattered over 13 kbp and the other ten exons encoding the C-half are clustered in a length of 4 kbp. Most introns in this gene occupy positions between or at the ends of the secondary structural elements, but they are not located at identical positions in the two protein-coding halves of the gene. When these exons are identified with their encoded functional subdomains, the exon arrangement shows a duplication pattern between the two halves of the gene. These data support, at the gene level, the hypothesis that mammalian PFK evolved from a prokaryotic progenitor by gene duplication and divergence.
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The NRAMP 1 gene is a major candidate gene influencing the outcome of infections with intracellular pathogens in numerous species. NRAMP 1 is highly conserved in many mammalian species and the NRAMP 1 gene shows considerable conservation in structure between mice and humans. The association of NRAMP 1 gene polymorphisms with disease in cattle has been limited to a single microsatellite located within the 3′-non coding region of the bovine NRAMP 1 gene. In order to facilitate further studies on this important gene, we now report the nearly complete structure of the bovine NRAMP 1 gene, including sizes and positions of 13 introns relative to the bovine NRAMP 1 gene coding sequence and the DNA sequence of intron–exon junctions. Comparison of the bovine, murine and human NRAMP 1 gene structures revealed a high degree of conservation in intron placement, though the lengths of several introns were less-well conserved. In general, the greatest divergence in intron lengths occurred in regions of the NRAMP 1 gene displaying the lowest coding sequence conservation. In addition, mutations near intron–exon junctions could account for 25 of the 75 total amino acid differences between murine and bovine NRAMP 1. Using information gained through this study, it was possible to rapidly identify a novel polymorphism within the bovine NRAMP 1 gene intron X. This polymorphism was shown by direct DNA sequence analysis to consist of insertion of three guanine nucleotides at positions 37, 40 and 98 relative to the intron X start point. Initial scans of several cattle breeds suggest that the two intron X alleles identified here are stable and widespread in the Bos taurus population.
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