Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing

Nucleic Acids Research

Volumn 29, Issue 11, 2001, Pages 2338-2348

  Brudno, Michael ^a,b   Gelfand, Mikhail S ^c   Spengler, Sylvia ^a   Zorn, Manfred ^a   Dubchak, Inna ^a,d   Conboy, John G ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b Stanford University   (United States)

^c STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^d NERSC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GUANINE; MESSENGER RNA PRECURSOR; NUCLEOTIDE; PYRIMIDINE; THYMINE; TRINUCLEOTIDE; URACIL;

ALGORITHM; ALTERNATIVE RNA SPLICING; ANALYTIC METHOD; ARTICLE; BRAIN TISSUE; CONTROLLED STUDY; ENHANCER REGION; EXON; GENE CASSETTE; GENE EXPRESSION; GENETIC REGULATION; INTRON; MUSCLE TISSUE; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TISSUE SPECIFICITY;

EID: 0035369805     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.11.2338     Document Type: Article

References (68)

1. Frequent alternative splicing of human genes
2. Alternative splicing of human genes: More the rule than the exception?
3. Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation
4. Alternative pre-mRNA splicing: The logic of combinatorial control
5. Neurexins: Three genes and 1001 products
6. Alternative splicing: A ubiquitous mechanism for the generation of multiple protein isoforms from single genes
7. Characterization of multiple isoforms of protein 4.1R expressed during erythroid terminal differentiation
8. The developmental consequences of alternate splicing in sex determination and differentiation in Drosophila
9. Secondary structure of splice sites in adenovirus mRNA precursors
10. A catalogue of splice junction sequences
11. Splicing of precursors to mRNAs by the spliceosomes
12. Prediction of function in DNA sequence analysis
13. Evaluation of gene structure prediction programs
14. Finding the genes in genomic DNA
15. Conserved quartets near 5′ intron junctions in primate nuclear pre-mRNA
16. G+C-rich tract in 5′ end of human introns
17. hnRNP proteins and the biogenesis of mRNA
18. hnRNP complexes: Composition, structure and function
19. The superfamily of arginine/serine-rich splicing factors
20. SR proteins and splicing control
21. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein
22. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability
23. A complex intronic splicing enhancer from the c-src pre-mRNA activates inclusion of a heterologous exon
24. Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element
25. Control of alternative pre-mRNA splicing by distributed pentameric repeats
26. Neuron-specific alternative splicing of nonmuscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence
27. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon
28. An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken β-tropomyosin pre-mRNA
29. Muscle-specific splicing enhancers regulate inclusion of the cardiac troponin T alternative exon in embryonic skeletal muscle
30. Disruption of splicing regulated by a CUG-binding protein in myotonic dystrophy
31. The tetranucleotide UCAY directs the specific recognition of RNA by the nova K-homology 3 domain
32. Conserved intron elements repress splicing of a neuron-specific c-src exon in vitro
33. Coordinate repression of a trio of neuron-specific splicing events by the splicing regulator PTB
34. Mutation of PTB binding sites causes misregulation of alternative 3′ splice site selection in vivo
35. RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
36. A sequence compilation and comparison of exons that are alternatively spliced in neurons
37. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer
38. RNA polymerase II and the integration of nuclear events
39. Conserved signals around the 5′ splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5′ and 3′ splice sites
40. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection
41. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames
42. The generally expressed hnRNP F is involved in a neural-specific pre-mRNA splicing event
43. Characterization of an intron splice enhancer that regulates alternative splicing of human GH pre-mRNA
44. A neuron-specific splicing switch mediated by an array of pre-mRNA repressor sites: Evidence of a regulatory role for the polypyrimidine tract binding protein and a brain-specific PTB counterpart
45. A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of nova to regulate neuron-specific alternative splicing
46. A neuron-specific isoform of brain ankyrin, 440-kD ankyrinB, is targeted to the axons of rat cerebellar neurons
47. Characterization of a brain-specific nuclear LIM domain protein (FHL1B) which is an alternatively spliced variant of FHL1
48. Primary structure of rat plasma membrane Ca(2+)-ATPase isoform 4 and analysis of alternative splicing patterns at splice site A
49. Alternative splicing of the sodium channel SCN8A predicts a truncated two-domain protein in fetal brain and non-neuronal cells
50. Amphiphysin II (SH3P9; BIN1), a member of the amphiphysin/Rvs family, is concentrated in the cortical cytomatrix of axon initial segments and nodes of ranvier in brain and around T tubules in skeletal muscle
51. Alternative splicing in the cytoplasmic II-III loop of the N-type Ca channel alpha 1B subunit: Functional differences are β subunit-specific
52. Alternatively spliced isoforms of the NMDARI receptor subunit
53. Clathrin light chain B: Gene structure and neuron-specific splicing
54. Reciprocal expression of myelin-associated glycoprotein splice variants in the adult human peripheral and central nervous systems
55. Genomic structure of the locus encoding protein 4.1. Structural basis for complex combinational patterns of tissue-specific alternative RNA splicing
56. Identification of B-KSR1, a novel brain-specific isoform of KSR1 that functions in neuronal signaling
57. Molecular cloning of a novel neuron-specific homologue of the erythrocyte membrane skeletal protein 4.1
58. Molecular and functional characterization of protein 4.1B, a novel member of the protein 4.1 family with high level, focal expression in brain
59. Identification of brain-specific splicing variants of the hDLG1 gene and altered splicing in neuroblastoma cell lines
60. Identification and differential regional expression of KOR-3/ORL-1 gene splice variants in mouse brain
61. Developmental regulation of highly active alternatively spliced forms of agrin
62. Expression of a developmentally-regulated neuron-specific isoform of the neurofibromatosis 1 (NF1) gene
63. LAR tyrosine phosphatase receptor: A developmental isoform is present in neurites and growth cones and its expression is regional-and cell-specific
64. Identification of a novel type II activin receptor, type IIA-N, induced during the neural differentiation of murine P19 embryonal carcinoma cells
65. Another mechanism for creating diversity in γ-aminobutyrate type A receptors: RNA splicing directs expression of two forms of γ 2 phosphorylation site
66. Conserved intron elements repress splicing of a neuron-specific c-src exon in vitro
67. A unique intronic splicing enhancer controls the inclusion of the agrin Y exon
68. Alternatively spliced isoforms of FE65 serve as neuron-specific and non-neuronal markers