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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
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Disease relevance of Pseudogenes


Psychiatry related information on Pseudogenes


High impact information on Pseudogenes

  • A pseudogene copy (SBDSP) with 97% nucleotide sequence identity resides in a locally duplicated genomic segment of 305 kb [8].
  • Of more than 1,000 human olfactory receptor genes, more than half seem to be pseudogenes [9].
  • More than two hundred characterized 21-hydroxylase deficiency alleles appear to result exclusively from sequence exchanges involving the 21-hydroxylase gene (CYP21B) and a closely related pseudogene (CYP21A) [10].
  • The sequenced 64 VH segments include 31 pseudogenes, of which 24 are highly conserved except for a few point mutations [11].
  • At least six new families of MER repeats and one pseudogene are intercalated within and between the Alu clusters [12].

Chemical compound and disease context of Pseudogenes

  • Rabies virus glycoprotein gene contains a long 3' noncoding region which lacks pseudogene properties [13].
  • The parallel evolution of trpEG pseudogenes in Buchnera of Diuraphis and certain other aphid hosts suggests that either selection at the host level is not effective or that fitness in these aphids is not limited by tryptophan availability [14].
  • Amplification of the mtp40 genome fragment and the presence of a guanine residue at position 285 in the oxyR pseudogene, demonstrated the infecting strain to be similar to present day M. tuberculosis isolates rather than to Mycobacterium bovis [15].
  • Although isoniazid has been used for the treatment of leprosy, it is shown here that the katG gene of Mycobacterium leprae is a pseudogene, which has probably been inactivated by multiple mutations [16].

Biological context of Pseudogenes

  • We previously demonstrated that pseudogenes complementary to the small nuclear RNAs U1, U2 and U3 are dispersed and abundant in the human genome [17].
  • We discuss the possible evolutionary origin of psi alpha 1 and other globin pseudogenes in the context of globin gene duplication [18].
  • Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene [19].
  • In the present study, a molecular analysis of a human genomic clone of PGK-2 originally isolated by Szabo et al. has revealed that this autosomal sequence completely lacks introns and contains characteristics of a processed gene, or 'retroposon', including the remnants of a poly(A)+ tail and bounding direct repeats [19].
  • In addition, we have detected a size polymorphism associated with the processed gene in the population, examined, and we have observed a region of apparent secondary structure homology between of 5' flanking region of the functional metallothionein-II gene and that of a mouse metallothionein-I gene [20].

Anatomical context of Pseudogenes


Associations of Pseudogenes with chemical compounds

  • The gene coding for the variant surface glycoprotein 20 of T. equiperdum is a late gene generated by the partial duplication of three silent pseudogenes [26].
  • (d) The new V beta 6.10 gene is probably a pseudogene, which may have been inactivated due to retrotransposition of Alu elements into its promoter region, a mutation affecting a highly conserved cysteine residue or mutations of the 3' recombinase signal sequence [27].
  • All nondeleted AQ0 allels had C4A-specific sequences and may thus be described as pseudogenes, whereas the nondeleted BQ0 alleles had C4A-instead of C4B-specific sequences [28].
  • 1 pseudogene 16.1 and result in an amino acid substitution at an invariant proline [29].
  • This strongly suggests that an ancestral HTF island at the pseudogene became methylated in the germline, and was lost due to the mutability of 5-methylcytosine [30].

Gene context of Pseudogenes


Analytical, diagnostic and therapeutic context of Pseudogenes

  • A fragment of 5.7 kilobases of this clone was completely sequenced and found to contain a pseudogene whose sequence is highly homologous to the sequences of known transplantation antigens [35].
  • Sequence analysis suggests that these genes or pseudogenes, which we designate zeta (zeta) and eta (eta), arose by a 794-base-pair tandem duplication followed by hundreds of exclusively cytosine to thymine mutations [36].
  • Restriction endonuclease mapping as well as partial nucleotide sequencing analysis revealed that the 21-OHase B gene of the patient has been converted to the pseudogene, 21-OHase A, as far as the critical 0.5-kb sequence was concerned [37].
  • Southern blot analysis of rat DNA using pP450PCN revealed that approximately 50 to 60 kilobases of DNA reacted with the PCN probe, suggesting the P-450PCN gene is either a very large gene or other genomic segments exist that react with the probe, such as pseudogenes or related P-450 genes that share homology [38].
  • Molecular cloning and characterization of a high affinity dopamine receptor (D1 beta) and its pseudogene [39].


  1. Rearrangements and point mutations of P450c21 genes are distinguished by five restriction endonuclease haplotypes identified by a new probing strategy in 57 families with congenital adrenal hyperplasia. Morel, Y., André, J., Uring-Lambert, B., Hauptmann, G., Bétuel, H., Tossi, M., Forest, M.G., David, M., Bertrand, J., Miller, W.L. J. Clin. Invest. (1989) [Pubmed]
  2. Simulating pseudogene evolution in vitro: determining the true number of mutations in a lineage. Vartanian, J.P., Henry, M., Wain-Hobson, S. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  3. Expressed cadherin pseudogenes are localized to the critical region of the spinal muscular atrophy gene. Selig, S., Bruno, S., Scharf, J.M., Wang, C.H., Vitale, E., Gilliam, T.C., Kunkel, L.M. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  4. Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens. Brayton, K.A., Knowles, D.P., McGuire, T.C., Palmer, G.H. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  5. Recombination events between the p47-phox gene and its highly homologous pseudogenes are the main cause of autosomal recessive chronic granulomatous disease. Roesler, J., Curnutte, J.T., Rae, J., Barrett, D., Patino, P., Chanock, S.J., Goerlach, A. Blood (2000) [Pubmed]
  6. Family relationships of murine major histocompatibility complex class I genes. Sequence of the T2Aa pseudogene, a member of gene family 3. Widmark, E., Ronne, H., Hammerling, U., Servenius, B., Larhammar, D., Gustafsson, K., Böhme, J., Peterson, P.A., Rask, L. J. Biol. Chem. (1988) [Pubmed]
  7. Evidence that two reports of mtDNA cytochrome c oxidase "mutations" in Alzheimer's disease are based on nDNA pseudogenes of recent evolutionary origin. Davis, J.N., Parker, W.D. Biochem. Biophys. Res. Commun. (1998) [Pubmed]
  8. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Boocock, G.R., Morrison, J.A., Popovic, M., Richards, N., Ellis, L., Durie, P.R., Rommens, J.M. Nat. Genet. (2003) [Pubmed]
  9. Different noses for different people. Menashe, I., Man, O., Lancet, D., Gilad, Y. Nat. Genet. (2003) [Pubmed]
  10. A de novo pathological point mutation at the 21-hydroxylase locus: implications for gene conversion in the human genome. Collier, S., Tassabehji, M., Sinnott, P., Strachan, T. Nat. Genet. (1993) [Pubmed]
  11. Structure and physical map of 64 variable segments in the 3'0.8-megabase region of the human immunoglobulin heavy-chain locus. Matsuda, F., Shin, E.K., Nagaoka, H., Matsumura, R., Haino, M., Fukita, Y., Taka-ishi, S., Imai, T., Riley, J.H., Anand, R. Nat. Genet. (1993) [Pubmed]
  12. Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment. Iris, F.J., Bougueleret, L., Prieur, S., Caterina, D., Primas, G., Perrot, V., Jurka, J., Rodriguez-Tome, P., Claverie, J.M., Dausset, J. Nat. Genet. (1993) [Pubmed]
  13. Rabies virus glycoprotein gene contains a long 3' noncoding region which lacks pseudogene properties. Ravkov, E.V., Smith, J.S., Nichol, S.T. Virology (1995) [Pubmed]
  14. Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis. Wernegreen, J.J., Moran, N.A. Proc. Biol. Sci. (2000) [Pubmed]
  15. Genotypic analysis of Mycobacterium tuberculosis from medieval human remains. Taylor, G.M., Goyal, M., Legge, A.J., Shaw, R.J., Young, D. Microbiology (Reading, Engl.) (1999) [Pubmed]
  16. On the catalase-peroxidase gene, katG, of Mycobacterium leprae and the implications for treatment of leprosy with isoniazid. Eiglmeier, K., Fsihi, H., Heym, B., Cole, S.T. FEMS Microbiol. Lett. (1997) [Pubmed]
  17. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Van Arsdell, S.W., Denison, R.A., Bernstein, L.B., Weiner, A.M., Manser, T., Gesteland, R.F. Cell (1981) [Pubmed]
  18. The structure of a human alpha-globin pseudogene and its relationship to alpha-globin gene duplication. Proudfoot, N.J., Maniatis, T. Cell (1980) [Pubmed]
  19. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. McCarrey, J.R., Thomas, K. Nature (1987) [Pubmed]
  20. Human metallothionein genes--primary structure of the metallothionein-II gene and a related processed gene. Karin, M., Richards, R.I. Nature (1982) [Pubmed]
  21. Human steroidogenic acute regulatory protein: functional activity in COS-1 cells, tissue-specific expression, and mapping of the structural gene to 8p11.2 and a pseudogene to chromosome 13. Sugawara, T., Holt, J.A., Driscoll, D., Strauss, J.F., Lin, D., Miller, W.L., Patterson, D., Clancy, K.P., Hart, I.M., Clark, B.J. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  22. Large-scale methylation analysis of human genomic DNA reveals tissue-specific differences between the methylation profiles of genes and pseudogenes. Grunau, C., Hindermann, W., Rosenthal, A. Hum. Mol. Genet. (2000) [Pubmed]
  23. Complete sequence of three alpha-tubulin cDNAs in Chinese hamster ovary cells: each encodes a distinct alpha-tubulin isoprotein. Elliott, E.M., Henderson, G., Sarangi, F., Ling, V. Mol. Cell. Biol. (1986) [Pubmed]
  24. Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss. Robertson, H.M. Genome Res. (1998) [Pubmed]
  25. Human profilin. Molecular cloning, sequence comparison, and chromosomal analysis. Kwiatkowski, D.J., Bruns, G.A. J. Biol. Chem. (1988) [Pubmed]
  26. Antigenic diversity by the recombination of pseudogenes. Thon, G., Baltz, T., Eisen, H. Genes Dev. (1989) [Pubmed]
  27. The genomic structure of human V beta 6 T cell antigen receptor genes. Li, Y., Szabo, P., Posnett, D.N. J. Exp. Med. (1991) [Pubmed]
  28. Null alleles of human complement C4. Evidence for pseudogenes at the C4A locus and for gene conversion at the C4B locus. Braun, L., Schneider, P.M., Giles, C.M., Bertrams, J., Rittner, C. J. Exp. Med. (1990) [Pubmed]
  29. Mutations in the human lambda5/14.1 gene result in B cell deficiency and agammaglobulinemia. Minegishi, Y., Coustan-Smith, E., Wang, Y.H., Cooper, M.D., Campana, D., Conley, M.E. J. Exp. Med. (1998) [Pubmed]
  30. Non-methylated CpG-rich islands at the human alpha-globin locus: implications for evolution of the alpha-globin pseudogene. Bird, A.P., Taggart, M.H., Nicholls, R.D., Higgs, D.R. EMBO J. (1987) [Pubmed]
  31. Gorilla class I major histocompatibility complex alleles: comparison to human and chimpanzee class I. Lawlor, D.A., Warren, E., Taylor, P., Parham, P. J. Exp. Med. (1991) [Pubmed]
  32. Immunohistochemical analysis reveals high frequency of PMS2 defects in colorectal cancer. Truninger, K., Menigatti, M., Luz, J., Russell, A., Haider, R., Gebbers, J.O., Bannwart, F., Yurtsever, H., Neuweiler, J., Riehle, H.M., Cattaruzza, M.S., Heinimann, K., Schär, P., Jiricny, J., Marra, G. Gastroenterology (2005) [Pubmed]
  33. Characterization of frequent deletions causing steroid 21-hydroxylase deficiency. White, P.C., Vitek, A., Dupont, B., New, M.I. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  34. Deletion of the entire cytochrome P450 CYP2D6 gene as a cause of impaired drug metabolism in poor metabolizers of the debrisoquine/sparteine polymorphism. Gaedigk, A., Blum, M., Gaedigk, R., Eichelbaum, M., Meyer, U.A. Am. J. Hum. Genet. (1991) [Pubmed]
  35. A pseudogene homologous to mouse transplantation antigens: transplantation antigens are encoded by eight exons that correlate with protein domains. Steinmetz, M., Moore, K.W., Frelinger, J.G., Sher, B.T., Shen, F.W., Boyse, E.A., Hood, L. Cell (1981) [Pubmed]
  36. DNA methylation at asymmetric sites is associated with numerous transition mutations. Selker, E.U., Stevens, J.N. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  37. Gene conversion-like events cause steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia. Harada, F., Kimura, A., Iwanaga, T., Shimozawa, K., Yata, J., Sasazuki, T. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  38. Cloning of DNA complementary to cytochrome P-450 induced by pregnenolone-16 alpha-carbonitrile. Characterization of its mRNA, gene, and induction response. Hardwick, J.P., Gonzalez, F.J., Kasper, C.B. J. Biol. Chem. (1983) [Pubmed]
  39. Molecular cloning and characterization of a high affinity dopamine receptor (D1 beta) and its pseudogene. Weinshank, R.L., Adham, N., Macchi, M., Olsen, M.A., Branchek, T.A., Hartig, P.R. J. Biol. Chem. (1991) [Pubmed]
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