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Genomes and Genes
| exonsSummarySummary: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or structural RNA. Top Publications
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Publications
Mapping and quantifying mammalian transcriptomes by RNA-SeqAli Mortazavi
Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
Nat Methods 5:621-8. 2008..Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' ..
RNA-Seq: a revolutionary tool for transcriptomicsZhong Wang
Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
Nat Rev Genet 10:57-63. 2009..This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes...- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Exome sequencing identifies the cause of a mendelian disorderSarah B Ng
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
Nat Genet 42:30-5. 2010..Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits... - Differential chromatin marking of introns and expressed exons by H3K36me3Paulina Kolasinska-Zwierz
The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
Nat Genet 41:376-81. 2009..We also observe a novel pattern: exons are preferentially marked with H3K36me3 relative to introns... - Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencingAndreas Gnirke
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Biotechnol 27:182-9. 2009..We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out... - Regulation of alternative splicing by histone modificationsReini F Luco
National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Science 327:996-1000. 2010..Histone marks affect splicing outcome by influencing the recruitment of splicing regulators via a chromatin-binding protein. These results outline an adaptor system for the reading of histone marks by the pre-mRNA splicing machinery... - HITS-CLIP yields genome-wide insights into brain alternative RNA processingDonny D Licatalosi
Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Nature 456:464-9. 2008..HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo... - Statistical significance for genomewide studiesJohn D Storey
Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 100:9440-5. 2003..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage... - Alternative isoform regulation in human tissue transcriptomesEric T Wang
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 456:470-6. 2008.... - Biased chromatin signatures around polyadenylation sites and exonsNoah Spies
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
Mol Cell 36:245-54. 2009..Conversely, exons were associated with distinct peaks in nucleosome density... - Ligand-independent androgen receptor variants derived from splicing of cryptic exons signify hormone-refractory prostate cancerRong Hu
Department of Urology, Oncology, and Pathology, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
Cancer Res 69:16-22. 2009..lacking the reading frames for the ligand-binding domain due to splicing of "intronic" cryptic exons to the upstream exons encoding the AR DNA-binding domain... 
Local dystrophin restoration with antisense oligonucleotide PRO051Judith C van Deutekom
Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
N Engl J Med 357:2677-86. 2007..We explored the safety, adverse-event profile, and local dystrophin-restoring effect of a single, intramuscular dose of an antisense oligonucleotide, PRO051, in patients with this disease...- Exon 1 of the HD gene with an expanded CAG repeat is sufficient to cause a progressive neurological phenotype in transgenic miceL Mangiarini
Division of Medical and Molecular Genetics, UMDS, Guy s Hospital, London, United Kingdom
Cell 87:493-506. 1996..This transgenic model will greatly assist in an eventual understanding of the molecular pathology of HD and may open the way to the testing of intervention strategies... - HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancerCharles J David
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
Nature 463:364-8. 2010..Our results thus define a pathway that regulates an alternative splicing event required for tumour cell proliferation... - Nucleosomes are well positioned in exons and carry characteristic histone modificationsRobin Andersson
The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
Genome Res 19:1732-41. 2009..Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression... - Alternative splicing and diseaseJamal Tazi
University of Montpellier II, Institute of Molecular Genetics, Centre Nationale de Recherche Scientifique, 1919 Route de Mende, France
Biochim Biophys Acta 1792:14-26. 2009..Here, we discuss well-studied examples that show how a disturbance of this balance can cause human disease. The rapidly emerging knowledge of splicing regulation now allows the development of treatment options... - Global analysis of nascent RNA reveals transcriptional pausing in terminal exonsFernando Carrillo Oesterreich
Max Planck Institute of Molecular Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
Mol Cell 40:571-81. 2010..Indeed, splicing catalysis is expected to occur posttranscriptionally in yeast, where the shortness of terminal exons should leave insufficient time for splicing. Here, we isolate endogenous S... - Mutations in the parkin gene cause autosomal recessive juvenile parkinsonismT Kitada
Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
Nature 392:605-8. 1998..The gene spans more than 500 kilobases and has 12 exons, five of which (exons 3-7) are deleted in the patient... - The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaOlivier Jaillon
Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
Nature 449:463-7. 2007..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants... - A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia veraChloe James
INSERM U362, Institut Gustave Roussy, Paris XI University, PR1, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France
Nature 434:1144-8. 2005..As this mutation is also found in other myeloproliferative disorders, this unique mutation will permit a new molecular classification of these disorders and novel therapeutical approaches... - AltAnalyze and DomainGraph: analyzing and visualizing exon expression dataDorothea Emig
Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
Nucleic Acids Res 38:W755-62. 2010..Our programs are available at http://www.altanalyze.org and http://www.domaingraph.de. These websites also include extensive documentation, tutorials and sample data... - Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease geneNara L M Sobreira
McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
PLoS Genet 6:e1000991. 2010..This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders... - Structure of PTB bound to RNA: specific binding and implications for splicing regulationFlorian C Oberstrass
Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
Science 309:2054-7. 2005..binding protein involved in multiple aspects of messenger RNA metabolism, including the repression of alternative exons. We have determined the solution structures of the four RNA binding domains (RBDs) of PTB, each bound to a CUCUCU .. - Evolving gene/transcript definitions significantly alter the interpretation of GeneChip dataManhong Dai
Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
Nucleic Acids Res 33:e175. 2005..It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions... - A slow RNA polymerase II affects alternative splicing in vivoManuel De la Mata
Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
Mol Cell 12:525-32. 2003..These results provide a direct proof for the elongation control of alternative splicing in vivo... - PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsMikita Suyama
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Nucleic Acids Res 34:W609-12. 2006..Another distinct feature is that the user can specify a subregion of the input alignment in order to specifically analyze functional domains or exons of interest. The PAL2NAL server is available at http://www.bork.embl.de/pal2nal. - Characterization and functional implications of the RNA binding properties of nuclear factor TDP-43, a novel splicing regulator of CFTR exon 9E Buratti
International Center for Genetic Engineering and Biotechnology ICGEB 34012 Trieste, Italy
J Biol Chem 276:36337-43. 2001..In particular, the highly conserved Phe residues in the first RRM region play a key role in nucleic acid recognition... - Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17M Hutton
Mayo Clinic Jacksonville, Florida 32224, USA
Nature 393:702-5. 1998..The increase in exon 10+ messenger RNA will increase the proportion of Tau containing four microtubule-binding repeats, which is consistent with the neuropathology described in several families with FTDP-17... - Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencingRyan Morin
Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
Biotechniques 45:81-94. 2008..of mRNA and individual exon abundance while simultaneously profiling the prevalence of both annotated and novel exons and exon-splicing events... - Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndromeChristian Gilissen
Department of Human Genetics, Institute for Genetic and Metabolic Disorders, Radboud University Nijmegen Medical Centre, The Netherlands
Am J Hum Genet 87:418-23. 2010..WDR35 is homologous to TULP4 (from the Tubby superfamily) and has previously been characterized as an intraflagellar transport component, confirming that Sensenbrenner syndrome is a ciliary disorder... - Systemic administration of PRO051 in Duchenne's muscular dystrophyNathalie M Goemans
Department of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
N Engl J Med 364:1513-22. 2011..The present phase 1-2a study aimed to assess the safety, pharmacokinetics, and molecular and clinical effects of systemically administered PRO051... - An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exonsJi Ann Lee
Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
Genes Dev 23:2284-93. 2009Neuronal depolarization and CaM kinase IV signaling alter the splicing of multiple exons in transcripts for ion channels, neurotransmitter receptors, and other synaptic proteins... - Proteolysis of mutant huntingtin produces an exon 1 fragment that accumulates as an aggregated protein in neuronal nuclei in Huntington diseaseChristian Landles
Department Medical and Molecular Genetics, King s College London School of Medicine, King s College London, London SE1 9RT, United Kingdom
J Biol Chem 285:8808-23. 2010..This methodology can be used to validate the inhibition of specific proteases as therapeutic targets for HD by pharmacological or genetic approaches... - Co-transcriptional splicing of constitutive and alternative exonsAmy Pandya-Jones
Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
RNA 15:1896-908. 2009..Using a quantitative RT-PCR assay, we show that the majority of introns separating constitutive exons are already excised from the human c-Src and fibronectin pre-mRNAs that are still in the process of synthesis, and .. - Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophyThai H Ho
Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
J Cell Sci 118:2923-33. 2005..We also find an immobile fraction of GFP-MBNL1 in DM1 fibroblasts and a similar rapid exchange in endogenous CUG RNA foci. Therefore, formation of RNA foci and disruption of MBNL1-regulated splicing are separable events... - A phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolutionSoochin Cho
Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48864, USA
Genome Res 14:1207-20. 2004..The small size of C. elegans introns should increase the rate at which each of these types of loss can occur, and might account for the dramatic difference in loss rate between nematodes and mammals... - Assessment of EGFR mutation status in lung adenocarcinoma by immunohistochemistry using antibodies specific to the two major forms of mutant EGFRMarie Brevet
Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
J Mol Diagn 12:169-76. 2010..IHC with EGFR mutant-specific antibodies could be used as a screen to identify most candidates for EGFR inhibitors... - TDP-43 binds heterogeneous nuclear ribonucleoprotein A/B through its C-terminal tail: an important region for the inhibition of cystic fibrosis transmembrane conductance regulator exon 9 splicingEmanuele Buratti
International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
J Biol Chem 280:37572-84. 2005..Finally, through splicing complex analysis, we show that splicing inhibition mediated by TDP-43 occurs at the earliest stages of spliceosomal assembly... - A novel mutation in the major intrinsic protein (MIP) associated with autosomal dominant congenital cataracts in a Chinese familyWei Wang
Eye Center of the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
Mol Vis 16:534-9. 2010..To detect the underlying genetic defect in a Chinese family affected with bilateral congenital cataracts... - Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicingSchraga Schwartz
Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
EMBO J 29:1629-36. 2010..In this review we discuss evidence for the coupling between transcription and splicing, focusing on recent findings suggesting a link between chromatin structure and splicing, and highlighting challenges this emerging field is facing... - A sensitive method for detecting EGFR mutations in non-small cell lung cancer samples with few tumor cellsMiguel A Molina-Vila
Catalan Institute of Oncology, Medical Oncology Service, Hosptial Germans Trias i Pujol, Badalona, Spain
J Thorac Oncol 3:1224-35. 2008..However, the number of tumor cells in a sample is often insufficient for EGFR assessment... - Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndromePeter M Krawitz
Max Planck Institute for Molecular Genetics, Berlin, Germany
Nat Genet 42:827-9. 2010..We identified homozygous or compound heterozygous mutations in PIGV in three additional families... - Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1Rachel Spellman
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
Mol Cell 27:420-34. 2007..Our data indicate crossregulation between PTB and its paralogs via nonproductive alternative splicing and a large degree of functional overlap between PTB and nPTB... - Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplificationJan P Schouten
MRC Holland, Hudsonstraat 68, 1057SN Amsterdam, The Netherlands
Nucleic Acids Res 30:e57. 2002..Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences... - TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencingJun ling Wang
Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
Brain 133:3510-8. 2010.... - Muscleblind-like 1 (Mbnl1) promotes insulin receptor exon 11 inclusion via binding to a downstream evolutionarily conserved intronic enhancerSupriya Sen
Medical Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California, USA
J Biol Chem 285:25426-37. 2010..Collectively, these findings demonstrate a role for Mbnl1 in controlling insulin receptor exon 11 inclusion via binding to a downstream intronic enhancer element... - Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault SyndromeSarah B Pierce
Department of Medicine, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 87:282-8. 2010.... - Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencingAnna Wetterbom
Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
Genome Biol 11:R78. 2010..We profile the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver, aiming to quantify expression of known genes and to identify novel transcribed regions... - A mouse model of osteochondromagenesis from clonal inactivation of Ext1 in chondrocytesKevin B Jones
Department of Orthopaedics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
Proc Natl Acad Sci U S A 107:2054-9. 2010..These results explain prior modeling failures with the necessity for somatic LOH in a developmentally regulated cell type... - Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumoursL A Donehower
Division of Molecular Virology, Baylor College of Medicine, Houston, Texas 77030
Nature 356:215-21. 1992.... - In-frame dystrophin following exon 51-skipping improves muscle pathology and function in the exon 52-deficient mdx mouseYoshitsugu Aoki
Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
Mol Ther 18:1995-2005. 2010..In-frame deletions of the hinge 3 region of the dystrophin protein, which is encoded by exons 50 and 51, are predicted to cause a variety of phenotypes... - A novel DNMT3B splice variant expressed in tumor and pluripotent cells modulates genomic DNA methylation patterns and displays altered DNA bindingSuhasni Gopalakrishnan
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
Mol Cancer Res 7:1622-34. 2009..Taken together, these results show that DNMT3B3Delta5 may play an important role in stem cell maintenance or differentiation and suggest that sequences encoded by exon 5 influence the functional properties of DNMT3B... - Formation of neuronal intranuclear inclusions underlies the neurological dysfunction in mice transgenic for the HD mutationS W Davies
Department of Anatomy and Developmental Biology, University College London, United Kingdom
Cell 90:537-48. 1997..The appearance in transgenic mice of these inclusions, followed by characteristic morphological change within neuronal nuclei, is strikingly similar to nuclear abnormalities observed in biopsy material from HD patients... - Nested Patch PCR enables highly multiplexed mutation discovery in candidate genesKatherine Elena Varley
Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
Genome Res 18:1844-50. 2008..In our pilot study, we amplified exons from colon cancer and matched normal human genomic DNA... - The germ cell nuclear proteins hnRNP G-T and RBMY activate a testis-specific exonYilei Liu
Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom
PLoS Genet 5:e1000707. 2009..In addition, we identified a high-affinity binding site for hnRNP G-T protein, showing it is also a sequence-specific RNA binding protein... - Molecular basis of iduronate-2-sulphatase gene mutations in patients with mucopolysaccharidosis type II (Hunter syndrome)P Li
Laboratory of Medical Genetics, University of Alabama at Birmingham, 35294, USA
J Med Genet 36:21-7. 1999..two splicing mutations (1006+5g-->c in intron 7, 1122C-->T in exon 8), and an intragenic deletion of IDS exons 4, 5, 6, and 7. Nine of the small mutations were novel mutations... - Adult-onset primary open-angle glaucoma caused by mutations in optineurinTayebeh Rezaie
Molecular Ophthalmic Genetics Laboratory, Surgical Research Center, Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA
Science 295:1077-9. 2002..Optineurin is expressed in trabecular meshwork, nonpigmented ciliary epithelium, retina, and brain, and we speculate that it plays a neuroprotective role... - Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13Ralph Burkhardt
Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY 10065, USA
Arterioscler Thromb Vasc Biol 28:2078-84. 2008..CONCLUSIONS: We identified variants in HMGCR that are associated with LDL-C across populations and affect alternative splicing of HMGCR exon13... - Enrichment of sequencing targets from the human genome by solution hybridizationRyan Tewhey
Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
Genome Biol 10:R116. 2009..9 Mb of sequence target. We demonstrate that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets. We obtained 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%... - Therapeutic modulation of DMD splicing by blocking exonic splicing enhancer sites with antisense oligonucleotidesA Aartsma-Rus
Department of Human Genetics, DMD Genetic Therapy Group, Leiden University Medical Center, 2333 AL Leiden, The Netherlands
Ann N Y Acad Sci 1082:74-6. 2006..of 121 AONs, of which 79 are effective in inducing the specific skipping of 38 out of the 79 different DMD exons. All AONs are located within exons and were hypothesized to act by steric hindrance of serine-arginine rich (SR) .. - Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosaRob W J Collin
Department of Human Genetics, Radboud University Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands
Am J Hum Genet 83:594-603. 2008..with 5'- and 3'- RACE analysis, resulted in the identification of a 10-kb transcript, starting with the annotated exons of EGFL11 and spanning 44 exons and 2 Mb of genomic DNA... - The human SLC8A3 gene and the tissue-specific Na+/Ca2+ exchanger 3 isoformsNadia Gabellini
Department of Biological Chemistry, University of Padova, Via G Colombo, 3, 35121 Padua, Italy
Gene 298:1-7. 2002..reverse transcriptase-polymerase chain reaction (RT-PCR) from the human neuroblastoma SH-SY5Y RNA, includes seven exons and encodes a protein of about 100 kDa... - Isolation of new splice isoforms, characterization and expression analysis of the human septin SEPT8 (KIAA0202)Susanne Bläser
Department of Pediatrics and Adolescent Medicine, University of Freiburg, Children s Hospital, Mathildenstrasse 1, D 79106 Freiburg, Germany
Gene 312:313-20. 2003..In addition, we performed the characterization of SEPT8 (KIAA0202) and identified new splice variants of SEPT8 (KIAA0202). The expression pattern of SEPT8 (KIAA0202) and its interaction partner SEPT5 (CDCrel-1) is illustrated... - Identification, genomic organization and mRNA expression of CRELD1, the founding member of a unique family of matricellular proteinsPaul A Rupp
Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97201, USA
Gene 293:47-57. 2002..The CRELD1 gene is deleted in the human cytogenetic disorder 3p- syndrome and is in the region of loss of heterozygosity for several types of cancer. A potential role for this protein in these disorders is discussed... - New human sodium/glucose cotransporter gene (KST1): identification, characterization, and mutation analysis in ICCA (infantile convulsions and choreoathetosis) and BFIC (benign familial infantile convulsions) familiesPatrice Roll
INSERM U491, Faculte de Medecine de la Timone, 27 Bd J Moulin, 13385, Marseille Cedex 5, France
Gene 285:141-8. 2002..The gene is divided into 16 exons and the predicted protein of 675 amino acids contains 14 transmembrane domains... - Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr geneBlagoy Blagoev
Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, M, DK 5230, Odense, Denmark
Gene 284:161-8. 2002..gene which shows that in addition to primary sequence homology, it shares a common genomic organization of coding exons with the murine IL-2 receptor common gamma chain (Il2rg)... - Molecular characterization of a second copy of holocarboxylase synthetase gene (hcs2) in Arabidopsis thalianaLaurence Denis
Laboratoire Mixte CNRS/INRA/Aventis (UMR 1932, Aventis CropScience, 14-20 rue Pierre Baizet, 69263 Lyon Cedex 9, France
J Biol Chem 277:10435-44. 2002..We discuss the possible role of such a multiplicity of putative HCS proteins in plants and discuss the involvement of each of hcs genes in the correct realization of biotinylation... - Human phosphodiesterase 8A splice variants: cloning, gene organization, and tissue distributionP Wang
Allergy Department, Schering Plough Research Institute, 2015 Galloping Hill Road, K 15 1600, Kenilworth, NJ 07033, USA
Gene 280:183-94. 2001..The PDE8A gene is revealed to contain 23 exons, and its exon-intron boundaries have been defined... - The RUNX3 gene--sequence, structure and regulated expressionC Bangsow
Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel
Gene 279:221-32. 2001..Transfection experiments demonstrated that both promoters were highly active in the GM1500 B-cell line, which endogenously expresses RUNX3, but were inactive in the K562 myeloid cell line, which does not express RUNX3... - Genomic organization of the human GRIK2 gene and evidence for multiple splicing variantsA Barbon
Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnologies, Brescia University Medical School, Via Valsabbina 19, 25123 Brescia, Italy
Gene 274:187-97. 2001..The GRIK2 gene was found to be split into 17 exons, covering about 670 kb of the region... - Mouse Atp6f, the gene encoding the 23-kDa proteolipid of vacuolar proton translocating ATPaseG H Sun-Wada
Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8 1, Ibaraki, Osaka 567 0047, Japan
Gene 274:93-9. 2001..to approximately 55 cM on chromosome 4, and its genomic organization is similar to that of the human gene: 8 exons separated by 7 introns, with boundaries matching the GT-AG rule... - Cloning and characterization of Disc1, the mouse ortholog of DISC1 (Disrupted-in-Schizophrenia 1)Lei Ma
Department of Neuroscience, West Point, Pennsylvania 19486, USA
Genomics 80:662-72. 2002..Identification of Disc1 will facilitate the study of DISC1's function and creation of mouse models of DISC1 disruption... - Identification of a novel human zinc finger protein gene ZNF313Yong Xin Ma
The Key Laboratory of Biotherapy, Ministry of Education, Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35:230-7. 2003..Total 6 exons of the human gene span a 17,484 bp genomic DNA sequence that was mapped to chromosome 20q13 by fluorescence in .. - Molecular cloning and initial characterization of the MG61/PORC gene, the human homologue of the Drosophila segment polarity gene PorcupineAndrea Caricasole
GlaxoSmithKline, Medicines Research Centre, Via Fleming 4, 37135 Verona, Italy
Gene 288:147-57. 2002..The human Porcupine locus (MG61/PORC) spans 15 exons over approximately 12 kb of genomic sequence on Xp11.23... - Molecular characterization and chromosomal assignment of the bovine glycinamide ribonucleotide formyltransferase (GART) gene on cattle chromosome 1q12.1-q12.2Anne Wohlke
Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17 p, 30559 Hannover, Germany
Gene 348:73-81. 2005..Cloning and characterization of the bovine GART gene revealed that the bovine gene consists of 23 exons spanning approximately 27 kb... - Genomic organization of the mouse Msh4 gene producing bicistronic, chimeric and antisense mRNAMasanori Hirano
Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 1 37 1 Kami Ikebukuro, Toshima ku, Tokyo 170 8455, Japan
Gene 342:165-77. 2004..Analysis of the exon-intron structures revealed unusual genomic organizations: the first three exons of delta and the first exon of epsilon are respectively mapped to the Hspa5 locus on chromosome 2 and the Pcbp3 .. - Structural organization of the mouse neurochondrin geneReiko Mochizuki-Sakisaka
Center for Tsukuba Advanced Research Alliance TARA, University of Tsukuba, Tsukuba, Ibaraki 305 8577, Japan
Int J Mol Med 14:361-6. 2004..It consists of 7 exons and spans about 10 kb; all splice junctions conform to the GT/AG rule... - Identification of 51 novel exons of the Usher syndrome type 2A (USH2A) gene that encode multiple conserved functional domains and that are mutated in patients with Usher syndrome type IIErwin Van Wijk
Department of Otorhinolaryngology, University Medical Center Nijmegen, Nijmegen, The Netherlands
Am J Hum Genet 74:738-44. 2004..Since mutation analysis by DNA sequencing of exons 1-21 revealed only ~63% of the expected USH2A mutations, we searched for so-far-uncharacterized exons of the gene... - Gene structure and evolution of Tieg3, a new member of the Tieg family of proteinsZiyuan Wang
Center of Anatomy, Department of Neuroanatomy, University of Goettingen, Kreuzbergring 36, 37075 Goettingen, Germany
Gene 325:25-34. 2004..The gene of mouse Tieg3 contains four exons. Due to the amino acid sequence similarity, mouse Tieg2 is regarded as an orthologue of human Tieg2... - Identification and characterization of C3orf6, a new conserved human gene mapping to chromosome 3q28G Vazza
Department of Biology, University of Padova, Via G Colombo, 3, 35131, Padua, Italy
Gene 314:113-20. 2003..C3orf6 gene is organised on 12 exons and the shorter transcript comes from an alternative splicing event skipping exon 6... - Molecular cloning, expression, and sequence analysis of GPRC6A, a novel family C G-protein-coupled receptorPetrine Wellendorph
Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, 2 Universitetsparken, DK 2100 Copenhagen, Denmark
Gene 335:37-46. 2004..Analysis of the intron-exon composition of the GPRC6A gene confirms that isoforms 2 and 3 are naturally occurring splice variants... - Tissue expression, protease specificity, and Kunitz domain functions of hepatocyte growth factor activator inhibitor-1B (HAI-1B), a new splice variant of HAI-1Daniel Kirchhofer
Department of Physiology, Genentech, Inc, South San Francisco, California 94080, USA
J Biol Chem 278:36341-9. 2003..Therefore, previously demonstrated roles of HAI-1 in various physiological and pathological processes likely involve both HAI-1B and HAI-1... - Characterization of cadherin-24, a novel alternatively spliced type II cadherinBryan J Katafiasz
University of Nebraska Medical Center, Department of Oral Biology, College of Dentistry and Eppley Cancer Center, Omaha, Nebraska 68198, USA
J Biol Chem 278:27513-9. 2003..In addition, aggregation assays show that both forms of cadherin-24 mediate strong cell-cell adhesion... - Molecular cloning of the mouse Ltbp-1 gene reveals tissue specific expression of alternatively spliced formsIrene Noguera
Department of Cell Biology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
Gene 308:31-41. 2003..The Ltbp-1 gene contains 34 exons and shows a similar organization to the LTBP-2 gene, suggesting that these genes originated from a common .. - Molecular structure and characterization of a novel murine ABC transporter, Abca13Scott A Barros
Curriculum in Toxicology, University of North Carolina at Chapel Hill, 27514, USA
Gene 307:191-200. 2003..The Abca13 gene consists of 44 exons which span 360 kb of genomic sequence. Abca13 has been mapped to mouse chromosome 11... - N34S mutation in the SPINK1 gene is not associated with alternative splicingAtsushi Masamune
Division of Gastroenterology, Tohoku University Graduate School of Medicine, Aoba ku, Sendai, Japan
Pancreas 34:423-8. 2007..The aberrant splicing caused by the cosegregating intronic mutations might play a role, but this hypothesis has not been tested. We here examined the messenger RNA sequences of the SPINK1 gene in patients carrying the mutations... - Mutation screening at the RNA level of the STK11/LKB1 gene in Peutz-Jeghers syndrome reveals complex splicing abnormalities and a novel mRNA isoform (STK11 c.597(insertion mark)598insIVS4)A A Abed
Department of Internal Medicine MGO Biocenter, University Halle Wittenberg, Halle, Germany
Hum Mutat 18:397-410. 2001..As a consequence of novel mutational mechanisms identified we discuss the impact of RNA based strategies for the detection of germinal STK11 mutations in PJS... - The genomic structure of the human SPEC1 gene reveals complex splicing and close promoter proximity to the AF1q translocation geneD M Pirone
Lombardi Cancer Center and the Department of Oncology, Georgetown University Medical Center, Washington, DC 20007, USA
Gene 273:295-303. 2001..of the genomic organization of SPEC1 revealed that the coding sequence of the SPEC1 isoform was derived from exons 2, 3 and 4, while the SPEC1-beta isoform was derived from exon 2 and a read-through event of intron 2... - The molecular basis of 3-methylcrotonylglycinuria, a disorder of leucine catabolismM E Gallardo
Centro de Investigaciones Biologicas CSIC, Universidad Autonoma de Madrid, Madrid, Spain
Am J Hum Genet 68:334-46. 2001.... - Alternative splicing in the human interleukin enhancer binding factor 3 (ILF3) geneN Duchange
Unité d Expression des Gènes Eucaryotes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, 15, Cedex, France
Gene 261:345-53. 2000..We used a GenBank sequence for the part of chromosome 19 corresponding to the ILF3 gene to determine the exon-intron organization of the entire gene which spans 38 kb and is divided into 21 exons. - Structural organization, complete genomic sequences and mutational analyses of the Fukuyama-type congenital muscular dystrophy gene, fukutinK Kobayashi
Laboratory of Genome Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
FEBS Lett 489:192-6. 2001..The fukutin genomic sequence spans approximately 100 kb and is organized into 10 exons (41-6067 bp) and nine introns (1841-21460 bp)... - The structure and expression of the human neuroligin-3 geneR A Philibert
Department of Psychiatry, University of Iowa, Rm 2 126b Psychiatry Research MEB, Iowa City, IA 52242 1000, USA
Gene 246:303-10. 2000..We now report the structure and the expression of that gene. The gene spans approximately 30kb and contains eight exons. Unlike the rat gene, it codes for at least two mRNAs and at least one of which is expressed outside the CNS... - Characterization of the mouse phenylalanine hydroxylase mutation Pah(enu3)M J Haefele
Department of Biological Sciences, Wichita State University, Wichita, Kansas 67260 0026, USA
Mol Genet Metab 72:27-30. 2001..The 5-nucleotide insertion and the 5-nucleotide deletion are both predicted to cause frame shifting in exon 12 and exon 13, leading to premature termination... - Molecular cloning of a novel human UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase, GalNAc-T8, and analysis as a candidate autosomal dominant hypophosphatemic rickets (ADHR) geneK E White
Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
Gene 246:347-56. 2000..Using exon-prediction analysis on genomic sequence from human chromosome 12p13.3, we identified novel exons that shared significant homology with the ppGaNTases... - Comparative genomic sequence analysis and isolation of human and mouse alternative EGFR transcripts encoding truncated receptor isoformsJ L Reiter
Tumor Biology Program, Mayo Clinic, Rochester, Minnesota 55905, USA
Genomics 71:1-20. 2001..We report that the EGFR gene spans nearly 200 kb and that the full-length 170-kDa EGFR is encoded by 28 exons. In addition, we have identified two human and two mouse alternative EGFR transcripts of 2.4-3... - Primary structure of human matrilin-2, chromosome location of the MATN2 gene and conservation of an AT-AC intron in matrilin genesS Muratoglu
Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
Cytogenet Cell Genet 90:323-7. 2000..Further, we identified in the human matrilin-2 gene a U12 type AT-AC intron between the last two exons encoding the oligomerization domain... - Characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1) mapping to 22q13.1V Trichet
Séquences Répétées et Centromères Humains, CNRS UPR 1142, Institut de Biologie, 4, bv Henri IV, 34060, Montpellier, France
Gene 257:109-17. 2000..A 4.8 kb transcript was found only in brain tissues. We present an interspecies sequence comparison, revealing three conserved domains, named TTLD1, TTLD2 and TTLD3, that are specific to the TTLs and TTL-like proteins... - Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat proteinJ Michaud
Division of Medical Genetics, University of Geneva Medical School, Geneva, Switzerland
Genomics 68:71-9. 2000To identify candidate genes for Down syndrome phenotypes or disorders that map to human chromosome 21q22.3, trapped exons are being used to isolate full-length transcripts... - RINX(VSX1), a novel homeobox gene expressed in the inner nuclear layer of the adult retinaT Hayashi
Department of Medicine, University of Washington, Seattle, Washington 98195, USA
Genomics 67:128-39. 2000..Since the RINX gene is likely an ortholog of the goldfish Vsx1 gene, it has been named VSX1 by the Human Gene Nomenclature Committee... - Human EMR2, a novel EGF-TM7 molecule on chromosome 19p13.1, is closely related to CD97H H Lin
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
Genomics 67:188-200. 2000..EMR2 fails to interact with CD55, the cellular ligand for CD97, suggesting the possibility of a different cellular ligand(s). EMR2 may therefore have a unique function in cells of monocyte/Mφ and granulocyte lineages...
Research Grants
- A Haplotype Map for Multiple SclerosisStephen L Hauser; Fiscal Year: 2010..In Specific Aim 3 we intend to generate high-coverage sequence information for the regulatory regions, exons and flanking regions of genes with unequivocal evidence of association for the discovery of rare variants ..
- CELLULAR MECHANISMS IN THE INDUCTION OF AROMATASECAROLE MENDELSON; Fiscal Year: 2009..of aromatase in each of these tissues is controlled by unique promoters that lie upstream of tissue-specific first exons that are alternatively spliced onto a common site in exon II...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2007Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the cytoplasm...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGADRIAN KRAINER; Fiscal Year: 2009Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the ..
- SMOOTH MUSCLE MYOSIN PHOSPHATASE SUBUNIT ISOFORMSSteven Fisher; Fiscal Year: 2007..isoforms are generated by tissue-specific and developmentally regulated cassette-type alternative splicing of exons. We hypothesized that regulated expression of MYPT isoforms determines smooth muscle phenotype-specific responses ..
- DEGRADATION OF OPIOID PEPTIDESLouis Hersh; Fiscal Year: 2000..neprilysin mRNAs which differ in their 5' untranslated sequence, and are generated from different non-coding exons utilizing different promoters...
- Tissue Factor Pathway Inhibitor Binding Proteins on EndoALAN MAST; Fiscal Year: 2005..Recombinant TFPI lacking the first two, non-translated, exons appears to be entirely secreted into the culture medium...
- BIOCHEMISTRY OF PRE-MRNA SPLICINGAdrian R Krainer; Fiscal Year: 2010Pre-mRNA splicing is an essential step in gene expression. It involves precise excision of introns and joining of exons from primary transcripts in the nucleus to generate mature mRNA, the template for protein synthesis in the ..
- Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetLen Pennacchio; Fiscal Year: 2009Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the ..
- Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetLen Pennacchio; Fiscal Year: 2009Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the ..
- Transcriptional elongation and splicing in human genes in situRichard A Padgett; Fiscal Year: 2010..For RNA splicing, very large introns present the problem of identifying the correct splice sites and exons in spite of a background of similar "decoy" sequences present within the introns...
- Translational Research in the DystrophinopathiesKevin Flanigan; Fiscal Year: 2002..Both are associated with mutations in the dystrophin gene, a huge gene with 79 exons spread over 2.4 million bases of genomic sequence...
- The Mammalian Cellular Splicing Machine - Structure and FunctionRuth Sperling; Fiscal Year: 2010..contain non-coding sequences (introns) that must be removed in order to accurately place the coding sequences (exons) in the correct reading frame...
- Comprehensive Mutational Analysis of the Cancer GenomeDennis Ballinger; Fiscal Year: 2004..utility of this approach, we propose in this Phase I application to analyze at single base resolution all coding exons from chromosomes 1p, 6, 15, and 18 (approximately 16% of the genome), in each of 12 CRC genomes...
- Nuclear Function of Abl in DNA Damage ResponseJean Y J Wang; Fiscal Year: 2010..approximately twenty thousand genes but encodes many more proteins through the alternative usage of variable exons. Alternative splicing has been shown to generate pro-death and anti-death protein isoforms from a single gene, ..
- Nuclear Function of Abl in DNA Damage ResponseJean Wang; Fiscal Year: 2009..approximately twenty thousand genes but encodes many more proteins through the alternative usage of variable exons. Alternative splicing has been shown to generate pro-death and anti-death protein isoforms from a single gene, ..
- The Catalytic Mechanism of Nuclear Premessenger RNA Splicing by the SpliceosomeJonathan P Staley; Fiscal Year: 2010..of the liberated 5'exon attacks the 3'splice site, excising the intron and ligating the flanking exons. The RNA components of the spliceosome have been implicated in both recognizing introns and catalyzing intron ..
- POSTTRANSCRIPTIONAL REGULATION OF ANGIOTENSIN RECEPTORSKathryn Sandberg; Fiscal Year: 2009..These transcripts are comprised of exons 1 and 3 (El,3) and exons 1, 2 and 3 (El,2,3)...
- Mechanisms Regulating Alternative pre-mRNA SplicingJames Patton; Fiscal Year: 2005..is remarkably efficient and rapid, an amazing feat considering that the signals that delineate introns from exons are not conserved in higher eukaryotes...
- CELLULAR MECHANISMS IN THE INDUCTION OF AROMATASECAROLE MENDELSON; Fiscal Year: 1999..The gene encoding human P450 is>75kb in size; the region encoding the P450 protein is contained within 9 exons (II-X)...
- Analyses of a Non tumorigenic Teratocarcinoma Cell LinePaulette McCormick; Fiscal Year: 2005..The predominant transcript, -2.3kb, contains two exons, the second of which is disrupted by the insertion...
- GENETICS AND MOLECULAR BIOLOGY OF MYOSINSANFORD BERNSTEIN; Fiscal Year: 1993..Alternative splicing of the RNA coding regions (exons) from this gene may lead to the production of up to 384 alternative forms (isoforms) of the MHC protein...
- DISSECTION OF THE FUNCTIONS OF HERPES SIMPLEX VIRUS ICPOBernard Roizman; Fiscal Year: 2007..ICP0 is encoded by 3 exons. ICP0 is encoded by 3 exons...