Analysis of the human VPS13 gene family

Genomics

Volumn 84, Issue 3, 2004, Pages 536-549

  Velayos Baeza, Antonio ^a   Vettori, Andrea ^b   Copley, Richard R ^a   Dobson Stone, Carol ^a   Monaco, A P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF PADOVA   (Italy)

Author keywords

Alternative splicing; Brain specific expression; CHAC; Chorea acanthocytosis; Chorein; COH1; Cohen syndrome; Gene duplication; Intramolecular duplication; VPS13

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME 15Q; CHROMOSOME 1P; CHROMOSOME 8Q; GENE; GENE EXPRESSION REGULATION; GENE LOCATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SPLICING; SEQUENCE HOMOLOGY; VPS13 GENE;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; BASE SEQUENCE; BLOTTING, NORTHERN; EVOLUTION, MOLECULAR; GENE COMPONENTS; GENE DUPLICATION; GENE EXPRESSION PROFILING; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VESICULAR TRANSPORT PROTEINS;

EID: 3843101623     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.04.012     Document Type: Article

References (37)

1. Rampoldi L., et al. A conserved sorting-associated protein is mutant in chorea-acanthocytosis. Nat. Genet. 28:2001;119-120
2. Ueno S., et al. The gene encoding a newly discovered protein, chorein, is mutated in chorea-acanthocytosis. Nat. Genet. 28:2001;121-122
3. Rampoldi L., Danek A., Monaco A.P. Clinical features and molecular bases of neuroacanthocytosis. J. Mol. Med. 80:2002;475-491
4. Redding K., Brickner J.H., Marschall L.G., Nichols J.W., Fuller R.S. Allele-specific suppression of a defective trans-Golgi network (TGN) localization signal in Kex2p identifies three genes involved in localization of TGN transmembrane proteins. Mol. Cell Biol. 16:1996;6208-6217
5. Brickner J.H., Fuller R.S. SOI1 encodes a novel, conserved protein that promotes TGN-endosomal cycling of Kex2p and other membrane proteins by modulating the function of two TGN localization signals. J. Cell Biol. 139:1997;23-36
6. Stege J.T., Laub M.T., Loomis W.F. Tip genes act in parallel pathways of early Dictyostelium development. Dev. Genet. 25:1999;64-77
7. Kolehmainen J., et al. Cohen syndrome is caused by mutations in a novel gene, COH1, encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport. Am. J. Hum. Genet. 72:2003;1359-1369
8. Wang C.W., et al. Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways. J. Biol. Chem. 276:2001;30442-30451
9. Modrek B., Lee C. A genomic view of alternative splicing. Nat. Genet. 30:2002;13-19
10. Kondrashov F.A., Koonin E.V. Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet. 19:2003;115-119
11. Dobson-Stone C., et al. Mutational spectrum of the CHAC gene in patients with chorea-acanthocytosis. Eur. J. Hum. Genet. 10:2002;773-781
12. Mironov A.A., Fickett J.W., Gelfand M.S. Frequent alternative splicing of human genes. Genome Res. 9:1999;1288-1293
13. Sorek R., Shamir R., Ast G. How prevalent is functional alternative splicing in the human genome? Trends Genet. 20:2004;68-71
14. Modrek B., Lee C.J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34:2003;177-180
15. Culbertson M.R. RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet. 15:1999;74-80
16. Wagner E., Lykke-Andersen J. mRNA surveillance: the perfect persist. J. Cell Sci. 115:2002;3033-3038
17. Lewis B.P., Green R.E., Brenner S.E. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. USA. 100:2003;189-192
18. Kondrashov F.A., Koonin E.V. Origin of alternative splicing by tandem exon duplication. Hum. Mol. Genet. 10:2001;2661-2669
19. Letunic I., Copley R.R., Bork P. Common exon duplication in animals and its role in alternative splicing. Hum. Mol. Genet. 11:2002;1561-1567
20. Grabowski P.J., Black D.L. Alternative RNA splicing in the nervous system. Prog. Neurobiol. 65:2001;289-308
21. Lee C.J., Irizarry K. Alternative splicing in the nervous system: an emerging source of diversity and regulation. Biol. Psychiatry. 54:2003;771-776
22. Copley R.R., Goodstadt L., Ponting C. Eukaryotic domain evolution inferred from genome comparisons. Curr. Opin. Genet. Dev. 13:2003;623-628
23. Hofmann K., Bucher P. The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. Trends Biochem. Sci. 21:1996;172-173
24. Bonifacino J.S., Traub L.M. Signals for sorting of transmembrane proteins to endosomes and lysosomes. Annu. Rev. Biochem. 72:2003;395-447
25. Hazes B. The (QxW)3 domain: a flexible lectin scaffold. Protein Sci. 5:1996;1490-1501
26. The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408:2000;796-815
27. Zhang J. Evolution by gene duplication: an update. Trends Ecol. Evol. 18:2003;292-298
28. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155
29. Prince V.E., Pickett F.B. Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3:2002;827-837
30. Copley R.R., Letunic I., Bork P. Genome and protein evolution in eukaryotes. Curr. Opin. Chem. Biol. 6:2002;39-45
31. Krylov D.M., Wolf Y.I., Rogozin I.B., Koonin E.V. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13:2003;2229-2235
32. Hedges S.B. The origin and evolution of model organisms. Nat. Rev. Genet. 3:2002;838-849
33. Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:2000;205-217
34. Goodstadt L., Ponting C.P. CHROMA: consensus-based colouring of multiple alignments for publication. Bioinformatics. 17:2001;845-846
35. Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:2002;502-504
36. Mott R. Accurate formula for P-values of gapped local sequence and profile alignments. J. Mol. Biol. 300:2000;649-659
37. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY