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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Open Reading Frames

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Disease relevance of Open Reading Frames

  • We report here the functional expression in E. coli of the entire single open reading frame of R2Bm and show that it encodes a double-stranded endo-nuclease (integrase) that can specifically cleave the 28S gene at the R2 insertion site [1].
  • The mRNAs for the 80 kd adenovirus preterminal protein (pTP) and the 140 kd DNA polymerase (AdPol) contain several exons spliced to the main open reading frames (m-ORFs) located in the early transcription unit E2B [2].
  • HPV-16 is actively transcribed in the cancers; the most abundant transcripts map to the E6 and E7 early open reading frames [3].
  • Fragile X syndrome is characterized at the molecular level by amplification of a (CGG)n repeat and hypermethylation of a CpG island preceeding the open reading frame of the fragile X gene (FMR-1) located in Xq27 [4].
  • We have identified a major gamma-herpesvirus-divergent locus (DL-B) in HHV-8 DNA encoding several HHV-8 unique open reading frames (ORFs), including a homologue of interleukin-6 (IL-6) and two homologues of macrophage inflammatory protein MIP-1 [5].

Psychiatry related information on Open Reading Frames


High impact information on Open Reading Frames

  • These data indicate that Pol II-associated Set2 methylates H3 providing a transcriptional memory which signals for deacetylation of ORFs by Rpd3S [11].
  • We localized jsd to a 272-kb region and resequenced this area to identify the underlying mutation: a frameshift that severely truncates the predicted protein product of a 2.3-kb genomic open reading frame [12].
  • In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames [13].
  • NBS1p70 is produced by internal translation initiation within the NBS1 mRNA using an open reading frame generated by the 657del5 frameshift [14].
  • Here we limit the minimum genetic region for STGD3 and adMD to a 0.6-cM interval by recombination breakpoint mapping and identify a single 5-bp deletion within the protein-coding region of a new retinal photoreceptor-specific gene, ELOVL4, in all affected members of STGD3 and adMD families [15].

Chemical compound and disease context of Open Reading Frames


Biological context of Open Reading Frames


Anatomical context of Open Reading Frames


Associations of Open Reading Frames with chemical compounds


Gene context of Open Reading Frames

  • The 5' leader of GCN4 mRNA contains four small open-reading-frames [36].
  • The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame [33].
  • Here, we report conditions that result in a dramatic transient increase in the rate of GCN4 protein synthesis, which also requires the prior translation of the 5' most proximal open reading frame but is independent of the GCN2 protein [37].
  • Gene lamB is followed by molA, an unidentified reading frame corresponding to a 131-amino-acid peptide with the characteristics of an exported protein [38].
  • The gene does not contain any significant conserved ORFs and thus does not appear to encode a protein, suggesting that XIST may function as a structural RNA within the nucleus [39].

Analytical, diagnostic and therapeutic context of Open Reading Frames


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  2. Nuclear transport of adenovirus DNA polymerase is facilitated by interaction with preterminal protein. Zhao, L.J., Padmanabhan, R. Cell (1988) [Pubmed]
  3. The human papillomavirus type 16 E7 gene encodes transactivation and transformation functions similar to those of adenovirus E1A. Phelps, W.C., Yee, C.L., Münger, K., Howley, P.M. Cell (1988) [Pubmed]
  4. The full mutation in the FMR-1 gene of male fragile X patients is absent in their sperm. Reyniers, E., Vits, L., De Boulle, K., Van Roy, B., Van Velzen, D., de Graaff, E., Verkerk, A.J., Jorens, H.Z., Darby, J.K., Oostra, B. Nat. Genet. (1993) [Pubmed]
  5. Kaposi's sarcoma-associated human herpesvirus-8 encodes homologues of macrophage inflammatory protein-1 and interleukin-6. Nicholas, J., Ruvolo, V.R., Burns, W.H., Sandford, G., Wan, X., Ciufo, D., Hendrickson, S.B., Guo, H.G., Hayward, G.S., Reitz, M.S. Nat. Med. (1997) [Pubmed]
  6. A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome. Mnatzakanian, G.N., Lohi, H., Munteanu, I., Alfred, S.E., Yamada, T., MacLeod, P.J., Jones, J.R., Scherer, S.W., Schanen, N.C., Friez, M.J., Vincent, J.B., Minassian, B.A. Nat. Genet. (2004) [Pubmed]
  7. Widespread expression of Huntington's disease gene (IT15) protein product. Sharp, A.H., Loev, S.J., Schilling, G., Li, S.H., Li, X.J., Bao, J., Wagster, M.V., Kotzuk, J.A., Steiner, J.P., Lo, A. Neuron (1995) [Pubmed]
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  9. Mutations in the open reading frame of the beta-site APP cleaving enzyme (BACE) locus are not a common cause of Alzheimer's disease. Nicolaou, M., Song, Y.Q., Sato, C.A., Orlacchio, A., Kawarai, T., Medeiros, H., Liang, Y., Sorbi, S., Richard, E., Rogaev, E.I., Moliaka, Y., Bruni, A.C., Jorge, R., Percy, M., Duara, R., Farrer, L.A., St Georg-Hyslop, P., Rogaeva, E.A. Neurogenetics (2001) [Pubmed]
  10. Identification by mRNA differential display of two up-regulated genes as candidate mediators of AIDS dementia. Wildemann, B., Haas, J., Stingele, K., Storch-HagenIocher, B., McArthur, J.C., Dawson, T.M., Dawson, V.L. Mol. Med. (2001) [Pubmed]
  11. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Carrozza, M.J., Li, B., Florens, L., Suganuma, T., Swanson, S.K., Lee, K.K., Shia, W.J., Anderson, S., Yates, J., Washburn, M.P., Workman, J.L. Cell (2005) [Pubmed]
  12. An X-to-autosome retrogene is required for spermatogenesis in mice. Bradley, J., Baltus, A., Skaletsky, H., Royce-Tolland, M., Dewar, K., Page, D.C. Nat. Genet. (2004) [Pubmed]
  13. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A., Bulyk, M.L. Nat. Genet. (2004) [Pubmed]
  14. An alternative mode of translation permits production of a variant NBS1 protein from the common Nijmegen breakage syndrome allele. Maser, R.S., Zinkel, R., Petrini, J.H. Nat. Genet. (2001) [Pubmed]
  15. A 5-bp deletion in ELOVL4 is associated with two related forms of autosomal dominant macular dystrophy. Zhang, K., Kniazeva, M., Han, M., Li, W., Yu, Z., Yang, Z., Li, Y., Metzker, M.L., Allikmets, R., Zack, D.J., Kakuk, L.E., Lagali, P.S., Wong, P.W., MacDonald, I.M., Sieving, P.A., Figueroa, D.J., Austin, C.P., Gould, R.J., Ayyagari, R., Petrukhin, K. Nat. Genet. (2001) [Pubmed]
  16. Complete nucleotide sequence of the AIDS virus, HTLV-III. Ratner, L., Haseltine, W., Patarca, R., Livak, K.J., Starcich, B., Josephs, S.F., Doran, E.R., Rafalski, J.A., Whitehorn, E.A., Baumeister, K. Nature (1985) [Pubmed]
  17. Single base deletion in the vasopressin gene is the cause of diabetes insipidus in Brattleboro rats. Schmale, H., Richter, D. Nature (1984) [Pubmed]
  18. Molecular cloning of the human CTP synthetase gene by functional complementation with purified human metaphase chromosomes. Yamauchi, M., Yamauchi, N., Meuth, M. EMBO J. (1990) [Pubmed]
  19. Expression of a beta-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast. Teem, J.L., Rosbash, M. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  20. Bacterial glutamate racemase has high sequence similarity with myoglobins and forms an equimolar inactive complex with hemin. Choi, S.Y., Esaki, N., Ashiuchi, M., Yoshimura, T., Soda, K. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  21. The t(4;11) chromosome translocation of human acute leukemias fuses the ALL-1 gene, related to Drosophila trithorax, to the AF-4 gene. Gu, Y., Nakamura, T., Alder, H., Prasad, R., Canaani, O., Cimino, G., Croce, C.M., Canaani, E. Cell (1992) [Pubmed]
  22. Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells. Turner, C.A., Mack, D.H., Davis, M.M. Cell (1994) [Pubmed]
  23. Essential large transcripts of the maize Spm transposable element are generated by alternative splicing. Masson, P., Rutherford, G., Banks, J.A., Fedoroff, N. Cell (1989) [Pubmed]
  24. napts, a mutation affecting sodium channel activity in Drosophila, is an allele of mle, a regulator of X chromosome transcription. Kernan, M.J., Kuroda, M.I., Kreber, R., Baker, B.S., Ganetzky, B. Cell (1991) [Pubmed]
  25. Expression of the split gene cob in yeast: evidence for a precursor of a "maturase" protein translated from intron 4 and preceding exons. Weiss-Brummer, B., Rödel, G., Schweyen, R.J., Kaudewitz, F. Cell (1982) [Pubmed]
  26. Characterization of the myotonic dystrophy region predicts multiple protein isoform-encoding mRNAs. Jansen, G., Mahadevan, M., Amemiya, C., Wormskamp, N., Segers, B., Hendriks, W., O'Hoy, K., Baird, S., Sabourin, L., Lennon, G. Nat. Genet. (1992) [Pubmed]
  27. A G-protein-coupled receptor for leukotriene B4 that mediates chemotaxis. Yokomizo, T., Izumi, T., Chang, K., Takuwa, Y., Shimizu, T. Nature (1997) [Pubmed]
  28. Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Gaba, A., Jacobson, A., Sachs, M.S. Mol. Cell (2005) [Pubmed]
  29. Identification of CCR8: a human monocyte and thymus receptor for the CC chemokine I-309. Tiffany, H.L., Lautens, L.L., Gao, J.L., Pease, J., Locati, M., Combadiere, C., Modi, W., Bonner, T.I., Murphy, P.M. J. Exp. Med. (1997) [Pubmed]
  30. Suppression cloning of the cDNA for a candidate subunit of a presynaptic calcium channel. Gundersen, C.B., Umbach, J.A. Neuron (1992) [Pubmed]
  31. Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5. Thomas, S.M., Lamb, R.A., Paterson, R.G. Cell (1988) [Pubmed]
  32. Nucleotide sequence of yeast LEU2 shows 5'-noncoding region has sequences cognate to leucine. Andreadis, A., Hsu, Y.P., Kohlhaw, G.B., Schimmel, P. Cell (1982) [Pubmed]
  33. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression. Werner, M., Feller, A., Messenguy, F., Piérard, A. Cell (1987) [Pubmed]
  34. Autosomal dominant cerebellar ataxia (SCA6) associated with small polyglutamine expansions in the alpha 1A-voltage-dependent calcium channel. Zhuchenko, O., Bailey, J., Bonnen, P., Ashizawa, T., Stockton, D.W., Amos, C., Dobyns, W.B., Subramony, S.H., Zoghbi, H.Y., Lee, C.C. Nat. Genet. (1997) [Pubmed]
  35. Structure and expression of the gene responsible for the triplet repeat disorder, dentatorubral and pallidoluysian atrophy (DRPLA). Nagafuchi, S., Yanagisawa, H., Ohsaki, E., Shirayama, T., Tadokoro, K., Inoue, T., Yamada, M. Nat. Genet. (1994) [Pubmed]
  36. Multiple upstream AUG codons mediate translational control of GCN4. Mueller, P.P., Hinnebusch, A.G. Cell (1986) [Pubmed]
  37. Coupling of GCN4 mRNA translational activation with decreased rates of polypeptide chain initiation. Tzamarias, D., Roussou, I., Thireos, G. Cell (1989) [Pubmed]
  38. Gene sequence of the lambda receptor, an outer membrane protein of E. coli K12. Clément, J.M., Hofnung, M. Cell (1981) [Pubmed]
  39. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafrenière, R.G., Xing, Y., Lawrence, J., Willard, H.F. Cell (1992) [Pubmed]
  40. smoothened encodes a receptor-like serpentine protein required for hedgehog signalling. van den Heuvel, M., Ingham, P.W. Nature (1996) [Pubmed]
  41. Molecular analysis of the En/Spm transposable element system of Zea mays. Pereira, A., Cuypers, H., Gierl, A., Schwarz-Sommer, Z., Saedler, H. EMBO J. (1986) [Pubmed]
  42. Evidence for an interaction between the CYP1(HAP1) activator and a cellular factor during heme-dependent transcriptional regulation in the yeast Saccharomyces cerevisiae. Fytlovich, S., Gervais, M., Agrimonti, C., Guiard, B. EMBO J. (1993) [Pubmed]
  43. Inhibition of calmodulin-dependent phosphodiesterase induces apoptosis in human leukemic cells. Jiang, X., Li, J., Paskind, M., Epstein, P.M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  44. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Wilson, M., DeRisi, J., Kristensen, H.H., Imboden, P., Rane, S., Brown, P.O., Schoolnik, G.K. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
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