Genome-wide detection of tissue-specific alternative splicing in the human transcriptome

Nucleic Acids Research

Volumn 30, Issue 17, 2002, Pages 3754-3766

  Xu, Qiang ^a   Modrek, Barmak ^a   Lee, Christopher ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; BRAIN; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENOME; HUMAN; HUMAN TISSUE; HYPERTENSION; LYMPH; METHODOLOGY; MUSCLE; PRIORITY JOURNAL; RETINA; SKIN; TESTIS; TISSUE SPECIFICITY;

EID: 0036712421     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf492     Document Type: Article

References (79)

1. Why genes in pieces?
2. Frequent alternative splicing of human genes
3. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
4. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
5. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome
6. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
7. Genome-wide analysis of alternative splicing using human expressed sequence data
8. Neuronatin mRNA: Alternatively spliced forms of a novel brain-specific mammalian developmental gene
9. Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene
10. Functional characterization of interferon regulatory factor 3a (IRF-3a), an alternative splice isoform of IRF-3
11. RNA processing and human disease
12. A new variant of glycoprotein CD44 confers metastatic potential to rat carcinoma cells
13. Tissue-specific alternative splicing of hybrid Shaker/lacZ genes correlates with kinetic differences in Shaker K+ currents in vivo
14. Differential subcellular localization, expression and biological toxicity of BRCA1 and the splice variant BRCA1-delta 11b
15. A variant of Alzheimer's disease with spastic paraparesis and unusual plaques due to deletion of exon 9 of presenilin 1
16. Alternative splicing and programmed cell death
17. hnRNP proteins and the biogenesis of mRNA
18. The superfamily of arginine/serine-rich splicing factors
19. SR proteins and splicing control
20. hnRNP complexes: Composition, structure, and function
21. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae
22. Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast
23. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability
24. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein
25. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing
26. An alternative-exon database and its statistical analysis
27. A genomic view of alternative splicing
28. Predicting splice variant from DNA chip expression data
29. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
30. Profiling alternative splicing on fiber-optic arrays
31. Pieces of the puzzle: Expressed sequence tags and the catalog of human genes
32. The GeneMine system for genome/proteome annotation and collaborative data-mining
33. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
34. SMART, a simple modular architecture research tool: Identification of signaling domains
35. Pfam: A comprehensive database of protein domain families based on seed alignments
36. The jackknife and the bootstrap for general stationary observations
37. Virus infection induces the assembly of coordinately activated transcription factors on the IFN-beta enhancer in vivo
38. Essential role of interferon regulatory factor 3 in direct activation of RANTES chemokine transcription
39. Dual utilization of an acceptor/donor splice site governs the alternative splicing of the IRF-3 gene
40. Interferon regulatory factor 3 and CREB-binding protein/p300 are subunits of double-stranded RNA-activated transcription factor DRAF1
41. Direct triggering of the type I interferon system by virus infection: Activation of a transcription factor complex containing IRF-3 and CBP/p300
42. Transgenic expression of IFN-alpha in the central nervous system of mice protects against lethal neurotropic viral infection but induces inflammation and neurodegeneration
43. Structural and functional neuropathology in transgenic mice with CNS expression of IFN-alpha
44. Alternative RNA splicing in the nervous system
45. Human membrane cofactor protein (MCP, CD46): Multiple isoforms and functions
46. Alternative pre-mRNA splicing: The logic of combinatorial control
47. WNK1, a novel mammalian serine/threonine protein kinase lacking the catalytic lysine in subdomain II
48. WNK kinases, a novel protein kinase subfamily in multi-cellular organisms
49. Human hypertension caused by mutations in WNK kinases
50. The human CDC42 gene: Genomic organization, evidence for the existence of a putative pseudogene and exclusion as a SJS1 candidate gene
51. Multiple roles for Cdc42 in cell regulation
52. The gamma-subunit of the coatomer complex binds Cdc42 to mediate transformation
53. Structure of the small G protein Cdc42 bound to the GTPase-binding domain of ACK
54. Genomic organization and chromosomal location of murine Cdc42
55. Nonclathrin coat protein gamma, a subunit of coatomer, binds to the cytoplasmic dilysine motif of membrane proteins. of the early secretory pathway
56. Coatomer is essential for retrieval of dilysine-tagged proteins to the endoplasmic reticulum
57. A single binding site for dilysine retrieval motifs and p23 within the gamma subunit of coatomer
58. A sequence compilation and comparison of exons that are alternatively spliced in neurons
59. Alternative gene form discovery and candidate gene selection from gene indexing projects
60. An extensive list of genes that produce alternative transcripts in the mouse
61. ASDB: Database of alternatively spliced genes
62. The intronerator: Exploring introns and alternative splicing in Caenorhabditis elegans
63. AsMamDB: An alternative splice database of mammals
64. A hidden Markov model for predicting transmembrane helices in protein sequences
65. Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation
66. Spontaneous frequency of exon skipping in the human HPRT gene
67. A new type of mutation causes a splicing defect in ATM
68. Genomic organization, expression, and alternate splicing of the mouse fatty aldehyde dehydrogenase gene
69. Fatty aldehyde dehydrogenase: Genomic structure, expression and mutation analysis in Sjogren-Larsson syndrome
70. Human variant glucose-6-phosphate transporter is active in microsomal transport
71. Quantitative analysis of glucose-6-phosphate translocase gene expression in various human tissues and haematopoietic progenitor cells
72. Gaucher disease: A G+1----A+1 IVS2 splice donor site mutation causing exon 2 skipping in the acid beta-glucosidase mRNA
73. The human Nramp2 gene: Characterization of the gene structure, alternative splicing, promoter region and polymorphisms
74. Heterologous expression, functional characterization and localization of two isoforms of the monkey iron transporter Nramp2
75. Profilin II is alternatively spliced, resulting in protilin isoforms that are differentially expressed and have distinct biochemical properties
76. Alternative splicing of the mouse profilin II gene generates functionally different profilin isoforms
77. Regulated splicing of an alternative exon of beta-tropomyosin pre-mRNAs in myogenic cells depends on the strength of pyrimidine-rich intronic enhancer elements
78. Characterization of tissue-specific LIM domain protein (FHL1C) which is an alternatively spliced isoform of a human LIM-only protein (FHL1)
79. Multiple splice forms of ribonuclease-inhibitor mRNA differ in the 5′-untranslated region