Comparative genomic analysis of the whale (Pseudorca crassidens) PRNP locus. 2008

Dae-Won Kim, and Sung-Hwa Chae, and Bo-Ra Kang, and Sang-Haeng Choi, and Aeri Kim, and Seonock Woo, and Hong-Seog Park
Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.

There have been many studies of the morphology, behavioral audiograms, and population structure of the false killer whale (Pseudorca crassidens), but sequencing, mapping, and functional and comparative genomics studies are still largely unknown. In this paper, we sequenced three novel BAC clones corresponding to a total length of 308 kb and spanning the PRNP, PRND, and RASSF2 loci, and conducted comparative genomic analysis to examine the genomic structure of the false killer whale PRNP locus. We determined that the three genes show a high degree of conservation in their syntenic regions with respect to gene order, gene orientation, and the predicted coding sequence (CDS) between human and whale, whereas PRNT was not detected in whale. Interestingly, the predicted CDS in whale PRNP contained a novel type of 4-copy octarepeat resulting from a 24 bp deletion when compared with the human sequence. In addition, we identified a novel 1869 bp repeat unit in a region that is non-syntenic to human and cow sequences and is therefore considered to be whale-specific sequence. Our results will provide novel insights into the genomic changes that have occurred during evolution of mammalian PRNP loci, and may also have implications for research into prion disease.

UI MeSH Term Description Entries
D007438 Introns Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes. Intervening Sequences,Sequences, Intervening,Intervening Sequence,Intron,Sequence, Intervening
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D011328 Prions Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL. Mink Encephalopathy Virus,Prion,Encephalopathy Virus, Mink
D004289 Dolphins Mammals of the families Delphinidae (ocean dolphins), Iniidae, Lipotidae, Pontoporiidae, and Platanistidae (all river dolphins). Among the most well-known species are the BOTTLE-NOSED DOLPHIN and the KILLER WHALE (a dolphin). The common name dolphin is applied to small cetaceans having a beaklike snout and a slender, streamlined body, whereas PORPOISES are small cetaceans with a blunt snout and rather stocky body. (From Walker's Mammals of the World, 5th ed, pp978-9) Amazon Dolphins,Baiji,Cephalorhynchus,Chinese River Dolphin,Delphinidae,False Killer Whale,Franciscana,Fraser's Dolphin,Ganges Dolphin,Gray Grampus,Humpback Dolphins,Irrawaddy River Dolphin,La Plata Dolphin,Lagenorhynchus,Lissodelphis,Many-Toothed Blackfish,Marine Dolphins,Melon-Headed Whale,Ocean Dolphins,Piebald Dolphins,Platanista,Pontoporia blainvillei,Pygmy Killer Whale,Right Whale Dolphins,Risso's Dolphin,Rough-Toothed Dolphin,Sousa,Susus,Tucuxi Dolphin,Whale, False Killer,Whale, Melon-Headed,Whale, Pygmy Killer,White-Beaked Dolphins,Amazon River Dolphins,Atlantic White-Sided Dolphins,Feresa attenuata,Ganges River Dolphin,Grampus griseus,Inia geoffrensis,Lagenodelphis hosei,Lagenorhynchus acutus,Lagenorhynchus albirostris,Langenorhynchus obliquidens,Lipotes vexillifer,Orcaella brevirostris,Pacific White-Sided Dolphins,Peponocephala electra,Planista gangetica,Pseudorca crassidens,Sotalia fluviatilis,Steno bredanensis,Yangtze River Dolphin,Atlantic White Sided Dolphins,Atlantic White-Sided Dolphin,Baijus,Dolphin,Dolphin, Fraser's,False Killer Whales,Franciscanas,Fraser Dolphin,Frasers Dolphin,Humpback Dolphin,Lagenodelphis hoseus,Lagenorhynchus albirostri,Langenorhynchus obliquiden,Lissodelphi,Many Toothed Blackfish,Marine Dolphin,Melon Headed Whale,Melon-Headed Whales,Ocean Dolphin,Orcaella brevirostri,Pacific White Sided Dolphins,Pacific White-Sided Dolphin,Piebald Dolphin,Planista gangeticas,Platanistas,Pontoporia blainvilleus,Pseudorca crassiden,Pygmy Killer Whales,Right Whale Dolphin,Risso Dolphin,Rissos Dolphin,Rough Toothed Dolphin,Rough-Toothed Dolphins,Sotalia fluviatili,Tucuxi Dolphins,White Beaked Dolphins,White-Beaked Dolphin
D005091 Exons The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA. Mini-Exon,Exon,Mini Exon,Mini-Exons
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D016133 Polymerase Chain Reaction In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. Anchored PCR,Inverse PCR,Nested PCR,PCR,Anchored Polymerase Chain Reaction,Inverse Polymerase Chain Reaction,Nested Polymerase Chain Reaction,PCR, Anchored,PCR, Inverse,PCR, Nested,Polymerase Chain Reactions,Reaction, Polymerase Chain,Reactions, Polymerase Chain
D017386 Sequence Homology, Amino Acid The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species. Homologous Sequences, Amino Acid,Amino Acid Sequence Homology,Homologs, Amino Acid Sequence,Homologs, Protein Sequence,Homology, Protein Sequence,Protein Sequence Homologs,Protein Sequence Homology,Sequence Homology, Protein,Homolog, Protein Sequence,Homologies, Protein Sequence,Protein Sequence Homolog,Protein Sequence Homologies,Sequence Homolog, Protein,Sequence Homologies, Protein,Sequence Homologs, Protein

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