Abstract
We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU...AG: rule with the exception of 1% of introns with :GC at their 5′ ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3′ splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3′ splice site was uridine. Consensus sequences for 5′ and 3′ splice sites and branchpoint sequences for Arabidopsis introns are presented.
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References
AhoAV, KerninghamBW, WeinbergerPJ: The AWK Programming Language. Addison Wesley, USA (1988).
BrownJWS: A catalogue of splice junction and putative branchpoint sequences from plant introns. Nucl Acids Res 14: 9549–9559 (1986).
FilipowiczW, GnaiadkowskiM, KlahreU, LiuH-X: Pre-mRNA splicing in plants. In: LamondA (ed) Pre-mRNA Processing, pp. 65–77. RG Landes Publishers, Georgetown, USA (1995).
GoodallGJ, FilipowiczW: The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58: 473–483 (1989).
GoodallGJ, FilipowiczW: The minimum length of pre-mRNA introns in monocots and dicots. Plant Mol Biol 14: 727–733 (1990).
GreenMR: Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu Rev Cell Biol 7: 559–599 (1991).
HudsonA: Fungal cytochrome C genes from plants. J Mol Biol 41: 1170–1171 (1995).
HuntAG, MogenBD, ChuNM, ChuaN-H: The SV40 small t is accurately and efficiently spliced in tobacco cells. Plant Mol Biol 16: 375–379 (1991).
JacksonI.J.: A reappraisel of non-consensus mRNA splice sites. Nucl Acids Res 19: 3795–3798 (1991).
KellerEB, NoonWA: Intron splicing: a conserved internal signal in introns of animal pre-mRNAs. Proc Natl Acad Sci USA 81: 7417–7420 (1984).
KrainerAR, ManiatisT: RNA splicing. In: HamesBD, GloverDM (eds) Transcription and Splicing, pp. 131–206. IRL Press, Oxford (1988).
LiJ, ZhaoJ, RoseAB, SchmidtR, LastRL: Arabidopsis phosphoribosylanthranilate isomerase: Molecular genetic analysis of triplicate tryptophan pathway genes. Plant Cell 7: 447–461 (1995).
LiuH-X, GoodallGA, KoleR, FilipowiczW: Effects of secondary structure on pre-mRNA splicing: Hairpins sequestering the 5′ but not the 3′ splice site inhibit intron processing in Nicotiana plumbaginifolia. EMBO J 14: 377–388 (1995).
LiuH-X, FilipowiczW: Mapping of branchpoint nucleotides in mutant pre-mRNAs expressed in plant cells. Plant J 9: 381–389 (1996).
LouH, McCulloughAJ, SchulerMA: 3′ splice site selection in dicot plant nuclei is position dependent. Mol Cell Biol 13: 4485–4493 (1993).
LuehrsenKR, TahaS, WalbotV: Nuclear pre-mRNA processing in higher plant. Prog Nucl Acid Res Mol Biol 47: 149–193 (1994).
MooreMJ, QueryCC, SharpPA: Splicing of precursors to messenger RNAs by the spliceosome. In: GestelandR, AtkinsJ (eds) The RNA World, pp. 303–358. Cold Spring Harbor Laboratory Press, USA (1993).
MountSM: A catalogue of splice junction sequences. Nucl. Acids Res. 10: 459–472 (1982).
NiyogiKK, FinkGR: Two anthranilate synthase genes in Arabidopsis: defense related regulation of the tryptophan pathway. Plant Cell 4: 721–733 (1992).
RymondBC, RosbashM: Yeast pre-mRNA splicing. In: JonesEW, PringleJR, BroachJR (eds) The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expressien, vol II, pp. 143–192. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1992).
SimpsonCG, BrownJWS: Efficient splicing of an AU-rich antisense intron sequence. Plant Mol Biol 21: 205–211 (1993).
Simpson CG, Leader DJ, Brown JWS: Plant intron sequences. In: Croy RRD (ed) Plant Molecular Biology, pp. 183–251. Bios Scientific Publishers, Oxford.
SimpsonCG, DavidsonD, ClarkGP, SmithPA, BrownJWS: Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency. Plant J 9: 369–380 (1996).
SmithCWJ, PorroEB, PattonJG, Nadal-GinardB: Scanning from an independently specified branchpoint defines the 3′ splice site of mammalian introns. Nature 342: 243–247 (1989).
SmithCWJ, ChuTT, Nadal-GinardB: Scanning and competition of AGs are involved in 3′ splice site selsction in mammalian introns. Mol Cell Biol 13: 4939–4952 (1993).
SullivanML, CarpenterTB, VierstraRD: Homologues of wheat ubiquitin-conjugating enzymes TaUBC1 and TaUBC4 are encoded by small multigene families in Arabidopsis thaliana. Plant Mol Biol 24: 651–661 (1994).
TanakaA, MitaS, OhtaS, KyozukaJ, ShimamotoJ, NakamuraK: Enhancement of foreign gene expression by a dicot intron in rice but not in tobacco is correlated with an increased level of mRNA and an efficient splicing of the intron. Nucl Acids Res 18: 6767–6770 (1990).
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Brown, J.W.S., Smith, P. & Simpson, C.G. Arabidopsis consensus intron sequences. Plant Mol Biol 32, 531–535 (1996). https://doi.org/10.1007/BF00019105
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DOI: https://doi.org/10.1007/BF00019105