'Exon' presentation slideshows

Detecting Alternative Splicing using the Human Affymetrix Exon Array 1.0

Detecting Alternative Splicing using the Human Affymetrix Exon Array 1.0. Instructors: Jennifer Barb, Zoila Rangel, Peter Munson June 15, 2009. Mathematical and Statistical Computing Laboratory Division of Computational Biosciences. Background. Gene structure.

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A markovian approach for the analysis of the gene structure

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Alternative splicing: A playground of evolution

Alternative splicing: A playground of evolution. Mikhail Gelfand Institute for Information Transmission Problems, RAS. May 2004. Alternative splicing of human (and mouse) genes. Alternative splicing of orthologous human and mouse genes

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On the biological significance of alternative splicing: a bioinformatics approach

On the biological significance of alternative splicing: a bioinformatics approach. Sandro J. de Souza TDR, 07/05/2004. RNA 10:757-765, 2004. Genomics. Bioinformatics. Large-scale Biology. The Real Revolution. Early 20 th century: Mendel and the inheritance laws

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Gene Recognition

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HJAY Human (Research) Junction Array

HJAY Human (Research) Junction Array. EURASNET, Cambridge Sept. 14 th , 2007 Tyson A. Clark. Typical Junction Array Design. Junction Arrays vs. Exon Arrays. Exon. Junction. Direct Measure of skipping events Reciprocal Analysis Multiple independent measurements of a single event

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Hidden Markov Models

Hidden Markov Models. CBB 231 / COMPSCI 261. What is an HMM?. An HMM is a stochastic machine M =( Q , ? , P t , P e ) consisting of the following: a finite set of states , Q ={ q 0 , q 1 , ... , q m } a finite alphabet ? ={ s 0 , s 1 , ... , s n }

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BIOINFORMATICS AND GENE DISCOVERY

UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL. Bioinformatics Tutorials. BIOINFORMATICS AND GENE DISCOVERY. Iosif Vaisman. 1998. From genes to proteins. From genes to proteins. DNA. PROMOTER ELEMENTS. TRANSCRIPTION. RNA. SPLICE SITES. SPLICING. mRNA. START CODON. STOP CODON.

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BIOINFORMATICS AND GENE DISCOVERY

UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL. Bioinformatics Tutorials. BIOINFORMATICS AND GENE DISCOVERY. Iosif Vaisman. 1998. From genes to proteins. From genes to proteins. DNA. PROMOTER ELEMENTS. TRANSCRIPTION. RNA. SPLICE SITES. SPLICING. mRNA. START CODON. STOP CODON.

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Hidden Markov Models

Hidden Markov Models. Slides by Bill Majoros, based on Methods for Computational Gene Prediction. What is an HMM?. An HMM is a stochastic machine M =( Q , ? , P t , P e ) consisting of the following: a finite set of states , Q ={ q 0 , q 1 , ... , q m }

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Gene Prediction: Similarity-Based Methods

Gene Prediction: Similarity-Based Methods. (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 15, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. Many slides are taken/adapted from http://www.bioalgorithms.info/slides.htm.

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Examples of pathways ...

ALTERNATIVE SPLICING. Examples of pathways. Irimia & Blencowe Curr Opin Cell Biol 24:323, 2012. Types of alternative splicing vary in frequency among eukaryotes. Kim Nucl Acids Res 35: 125, 2006. Chen & Manley, 2009. Chen & Manley, 2009. How are different splicing pathways selected?.

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Mutation scanning in Marfan syndrome using High Resolution Melt analysis

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Fumarate Hydratase; One Gene, Two Inheritance Patterns and Two or Three Diseases

Fumarate Hydratase; One Gene, Two Inheritance Patterns and Two or Three Diseases. Oliver Ridgway West Midlands Regional Genetics Laboratory. Fumarate hydratase (FH). 1q42.1 10 exons ~22 kb of DNA Transcript length of 1,790bp 510 amino acids Cytosolic and mitochondrial forms

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Patterns of Dystrophin Gene Deletion/Duplication in a Sample of Saudi Patients with Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder that affects 1 in 3,500 males and is caused by mutations in the dystrophin gene. The gene is the largest in the human genome, encompassing 2.6 million base pairs of DNAs and containing 79 exons. DMD occurs either due to nonsense mutations (premature stop codons) or by large rearrangements (deletions or duplications) that disturb the reading frame of the dystrophin gene and in consequence abolish the production of dystrophin in muscles [1].

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5/1833

10kb. 50kb. inverted region. 10kb. (393). (84). (+365). 389. 75. 609. 183. 60. 204. 249. 99. 195. 93. 264. 399. TC3F. TC3R. TB2R. 0cM. RE. EP. PP. IF2. FIP. OXI. CAS. ANK. PUM. MYB. GAG. PME. REV. PUM. 26SP. RHZF. (77). LRRPK. 575. 69. 621. 183. 60.

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Splice Signal in Alternatively Spliced Exons

Splice Signal in Alternatively Spliced Exons. by George Su (gpsu@ucsd.edu) Advisor: Vineet Bafna (vbafna@cs.ucsd.edu) Shaojie Zhang (shzhang@cs.ucsd.edu). Question: Is there a signal that characterizes alternatively spliced exons from constitutively spliced exons? We focus on exon-skipping.

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Name:_______________

Quiz 7: Biol 203 Fall 2013. The Arristaless-like (Arl) gene below carries a homeodomain DNA binding domain (HD). Furthermore, it has a proven activator domain (A) and repressor domain (R). cDNAs with A-R-HD reveal no function, however, cDNAs with A-HD have activator like

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151

A. Exon A. B. 1. 2. 3. 4. 5. H. D. S. *. 3638. 500. 120. 673. Isoform 4 (NM_0017509) (classical form). 31 43. 151. 284. 507. 153. 137. *. *. *. 3638. 500. 238. 673. Isoform 1 (NM_023006) (exon 3 truncation). 166. 151. 31 43. 660. 3 134. *. *.

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13-4

400 bp. 300 bp. 13-1. 13-2. 13-3. 13-4. 13-5. 13-6. 13-7. 13-8. 13-9. 13-10. 13-11. Figure (E)F-1. Agarose gel electrophoresis of GLRA1 exon 6 amplimers. This exon is amplified in all except affected individuals in Family 1. Expected amplimer size for exon 6 is 315 bp.

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