RNA Splice Junctions of Different Classes of Eukaryotes: Sequence Statistics and Functional Implications in Gene Expression

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1987 Sep 11

PMID 3658675

Citations 711

Authors

M B Shapiro

P Senapathy

Affiliations

Soon will be listed here.

Abstract

A systematic analysis of the RNA splice junction sequences of eukaryotic protein coding genes was carried out using the GENBANK databank. Nucleotide frequencies obtained for the highly conserved regions around the splice sites for different categories of organisms closely agree with each other. A striking similarity among the rare splice junctions which do not contain AG at the 3' splice site or GT at the 5' splice site indicates the existence of special mechanisms to recognize them, and that these unique signals may be involved in crucial gene-regulation events and in differentiation. A method was developed to predict potential exons in a bare sequence, using a scoring and ranking scheme based on nucleotide weight tables. This method was used to find a majority of the exons in selected known genes, and also predicted potential new exons which may be used in alternative splicing situations.

Citing Articles

Novel Splice-Altering Variants in the and Genes Causative of X-Linked Choroideremia and Cone Dystrophy.

Ridgeway A, Shortall C, Finnegan L, Long R, Matthews E, Dockery A Genes (Basel). 2025; 16(1).

PMID: 39858572 PMC: 11764614. DOI: 10.3390/genes16010025.

From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites.

Vorechovsky I J Hum Genet. 2024; 70(3):125-133.

PMID: 39639151 PMC: 11802449. DOI: 10.1038/s10038-024-01308-8.

RNA Splicing Aberrations in Hereditary Cancer: Insights from Turkish Patients.

Kilic S, Sukruoglu Erdogan O, Tuncer S, Celik Demirbas B, Yalniz Kayim Z, Yazici H Curr Issues Mol Biol. 2024; 46(11):13252-13266.

PMID: 39590384 PMC: 11593161. DOI: 10.3390/cimb46110790.

Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration.

Sangermano R, Gupta P, Price C, Han J, Navarro J, Condroyer C NPJ Genom Med. 2024; 9(1):58.

PMID: 39516462 PMC: 11549414. DOI: 10.1038/s41525-024-00439-3.

From computational models of the splicing code to regulatory mechanisms and therapeutic implications.

Capitanchik C, Wilkins O, Wagner N, Gagneur J, Ule J Nat Rev Genet. 2024; 26(3):171-190.

PMID: 39358547 DOI: 10.1038/s41576-024-00774-2.

References

Sharp P . Splicing of messenger RNA precursors. Science. 1987; 235(4790):766-71. DOI: 10.1126/science.3544217. View

Harr R, Haggstrom M, Gustafsson P . Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res. 1983; 11(9):2943-57. PMC: 325935. DOI: 10.1093/nar/11.9.2943. View

Iida Y, Sasaki F . Recognition patterns for exon-intron junctions in higher organisms as revealed by a computer search. J Biochem. 1983; 94(6):1731-8. DOI: 10.1093/oxfordjournals.jbchem.a134524. View

Erbil C, Niessing J . The primary structure of the duck alpha D-globin gene: an unusual 5' splice junction sequence. EMBO J. 1983; 2(8):1339-43. PMC: 555280. DOI: 10.1002/j.1460-2075.1983.tb01589.x. View

Senapathy P . Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications. Proc Natl Acad Sci U S A. 1986; 83(7):2133-7. PMC: 323245. DOI: 10.1073/pnas.83.7.2133. View

Staden R . Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 1984; 12(1 Pt 2):505-19. PMC: 321067. DOI: 10.1093/nar/12.1part2.505. View

Wieringa B, Meyer F, Reiser J, Weissmann C . Unusual splice sites revealed by mutagenic inactivation of an authentic splice site of the rabbit beta-globin gene. Nature. 1983; 301(5895):38-43. DOI: 10.1038/301038a0. View

Green M . Pre-mRNA splicing. Annu Rev Genet. 1986; 20:671-708. DOI: 10.1146/annurev.ge.20.120186.003323. View

Emorine L, DREHER K, Kindt T, Max E . Rabbit immunoglobulin kappa genes: structure of a germline b4 allotype J-C locus and evidence for several b4-related sequences in the rabbit genome. Proc Natl Acad Sci U S A. 1983; 80(18):5709-13. PMC: 384328. DOI: 10.1073/pnas.80.18.5709. View

10.

Bernard O, Hozumi N, Tonegawa S . Sequences of mouse immunoglobulin light chain genes before and after somatic changes. Cell. 1978; 15(4):1133-44. DOI: 10.1016/0092-8674(78)90041-7. View

11.

Kim S, Davis M, Sinn E, Patten P, Hood L . Antibody diversity: somatic hypermutation of rearranged VH genes. Cell. 1981; 27(3 Pt 2):573-81. DOI: 10.1016/0092-8674(81)90399-8. View

12.

Heidmann O, Rougeon F . Diversity in the rabbit immunoglobulin kappa chain variable regions is amplified by nucleotide deletions and insertions at the V-J junction. Cell. 1983; 34(3):767-77. DOI: 10.1016/0092-8674(83)90533-0. View

13.

Mount S . A catalogue of splice junction sequences. Nucleic Acids Res. 1982; 10(2):459-72. PMC: 326150. DOI: 10.1093/nar/10.2.459. View

14.

Shibahara S, Kubo T, Perski H, Takahashi H, Noda M, Numa S . Cloning and sequence analysis of human genomic DNA encoding gamma subunit precursor of muscle acetylcholine receptor. Eur J Biochem. 1985; 146(1):15-22. DOI: 10.1111/j.1432-1033.1985.tb08614.x. View

15.

Kwoh T, Engler J . The nucleotide sequence of the chicken thymidine kinase gene and the relationship of its predicted polypeptide to that of the vaccinia virus thymidine kinase. Nucleic Acids Res. 1984; 12(9):3959-71. PMC: 318803. DOI: 10.1093/nar/12.9.3959. View

16.

Max E, Seidman J, Leder P . Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene. Proc Natl Acad Sci U S A. 1979; 76(7):3450-4. PMC: 383843. DOI: 10.1073/pnas.76.7.3450. View

17.

Brown J . A catalogue of splice junction and putative branch point sequences from plant introns. Nucleic Acids Res. 1986; 14(24):9549-59. PMC: 341320. DOI: 10.1093/nar/14.24.9549. View

18.

Karn J, Brenner S, Barnett L . Protein structural domains in the Caenorhabditis elegans unc-54 myosin heavy chain gene are not separated by introns. Proc Natl Acad Sci U S A. 1983; 80(14):4253-7. PMC: 384015. DOI: 10.1073/pnas.80.14.4253. View

19.

Sakano H, Huppi K, Heinrich G, Tonegawa S . Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979; 280(5720):288-94. DOI: 10.1038/280288a0. View

20.

Hozumi N, Hawley R, Murialdo H . Molecular cloning of an immunoglobulin kappa constant gene from NZB mouse. Gene. 1981; 13(2):163-172. DOI: 10.1016/0378-1119(81)90005-6. View