Lab 11: Simple genomic data analysis using R 1. UCSC genome
... Select “Table Browser” under the “Tool” menu. In the table browser page, select: “Mammal” under clade, “Human” under genome, “Mar. 2006 (NCBI36/hg18)” assembly, “Genes and Gene Prediction” under group, “RefSeq Genes” under track, “refGene” under table. Then select “genome” under region, which means: ...
... Select “Table Browser” under the “Tool” menu. In the table browser page, select: “Mammal” under clade, “Human” under genome, “Mar. 2006 (NCBI36/hg18)” assembly, “Genes and Gene Prediction” under group, “RefSeq Genes” under track, “refGene” under table. Then select “genome” under region, which means: ...
Eukaryotic Genes and Genomes I
... is ~ 3000 million base pairs, or ~ 3,000 Mb, i.e., ~ 3 billion base pairs. In other words, there is about 100-fold more DNA in the human genome than is required for encoding 22,500 proteins. What is it all doing? Some of it constitutes promoters upstream of each gene, some is structural DNA around c ...
... is ~ 3000 million base pairs, or ~ 3,000 Mb, i.e., ~ 3 billion base pairs. In other words, there is about 100-fold more DNA in the human genome than is required for encoding 22,500 proteins. What is it all doing? Some of it constitutes promoters upstream of each gene, some is structural DNA around c ...
DNA Structure and Replication
... expressed, interrupt most eukaryotic genes • Exons = portions of a gene that are expressed ...
... expressed, interrupt most eukaryotic genes • Exons = portions of a gene that are expressed ...
Lecture 7 Mutation and genetic variation
... • one important mechanism generating duplications is unequal crossing over. ...
... • one important mechanism generating duplications is unequal crossing over. ...
Slide 1
... The gene is controlled by a promoter (p) which is not simple – there are generalized transcription factors and more gene-specific ones that may reside outside of the promoter proper, within the gene, within the 3’ end of the gene or even far 5’ and/or 3’ of the gene itself –they open the DNA and exp ...
... The gene is controlled by a promoter (p) which is not simple – there are generalized transcription factors and more gene-specific ones that may reside outside of the promoter proper, within the gene, within the 3’ end of the gene or even far 5’ and/or 3’ of the gene itself –they open the DNA and exp ...
file - Athens Academy
... Zea mays has ten chromosomes, and in a small percentage of both domesticated maize and teosinte the normal chromosome 10 (N10) has been replaced with abnormal chromosome 10 (Ab10). Ab10 is defined cytogenetically by the addition of a terminal piece of foreign DNA onto the long arm of N10. This piece ...
... Zea mays has ten chromosomes, and in a small percentage of both domesticated maize and teosinte the normal chromosome 10 (N10) has been replaced with abnormal chromosome 10 (Ab10). Ab10 is defined cytogenetically by the addition of a terminal piece of foreign DNA onto the long arm of N10. This piece ...
Document
... 17) CDS is an abbreviation for ________________________. 18a) Can all CDS’ be said to contain an ORF? (yes, no-circle one) 18b) Can all ORFs be said to contain a CDS? (yes, no-circle one) ...
... 17) CDS is an abbreviation for ________________________. 18a) Can all CDS’ be said to contain an ORF? (yes, no-circle one) 18b) Can all ORFs be said to contain a CDS? (yes, no-circle one) ...
seminar
... • Pseudogenes confound HMM and homology based gene prediction. • Processed pseudogenes can be identified by: – Lack of introns (but ~20% of real genes lack introns) – Not being the best place in genome an mRNA aligns (be careful not to filter out real paralogs) – Being inserted from another chromoso ...
... • Pseudogenes confound HMM and homology based gene prediction. • Processed pseudogenes can be identified by: – Lack of introns (but ~20% of real genes lack introns) – Not being the best place in genome an mRNA aligns (be careful not to filter out real paralogs) – Being inserted from another chromoso ...
Finding Protein-Coding Genes
... The purpose of this exercise is to illustrate some of the concepts in the lectures and readings by using web servers to annotate genes. As with all my assignments, if your interests lead you in a different direction, you are free to follow that direction as long as it deals with gene annotation. You ...
... The purpose of this exercise is to illustrate some of the concepts in the lectures and readings by using web servers to annotate genes. As with all my assignments, if your interests lead you in a different direction, you are free to follow that direction as long as it deals with gene annotation. You ...
Document
... _____ 2. In the lac operon of E. coli, lactose functions as a. a promoter. b.an operator. c. a repressor protein d. an inducer. _____ 3. In eukaryotic cells, transcription occurs a. on parts of the DNA that are uncoiled. c. b. only on introns. d. ...
... _____ 2. In the lac operon of E. coli, lactose functions as a. a promoter. b.an operator. c. a repressor protein d. an inducer. _____ 3. In eukaryotic cells, transcription occurs a. on parts of the DNA that are uncoiled. c. b. only on introns. d. ...
Chapter 21
... Replication of a strand transfer complex generates a cointegrate, which is a fusion of the donor and target replicons. The cointegrate has two copies of the transposon, which lie between the original replicons. Recombination between the transposon copies regenerates the original replicons, but the r ...
... Replication of a strand transfer complex generates a cointegrate, which is a fusion of the donor and target replicons. The cointegrate has two copies of the transposon, which lie between the original replicons. Recombination between the transposon copies regenerates the original replicons, but the r ...
Gene action
... General idea: the closer the relationship between two species, the more similar their DNA code will be Therefore, by finding out the genome of many species, we can not only work out relationships, but also identify the rise of different alleles! ...
... General idea: the closer the relationship between two species, the more similar their DNA code will be Therefore, by finding out the genome of many species, we can not only work out relationships, but also identify the rise of different alleles! ...
TALK
... • Genome streamlining occurs when selection is able to act to directly reduce the amount of DNA which serves no useful function for the cell. Introns, inteins, transposons and pesudogenes are examples of "selfish DNA", which persist because their impact on cellular replication efficiency is too smal ...
... • Genome streamlining occurs when selection is able to act to directly reduce the amount of DNA which serves no useful function for the cell. Introns, inteins, transposons and pesudogenes are examples of "selfish DNA", which persist because their impact on cellular replication efficiency is too smal ...
How hereditary information is stored in the genome.
... that provides special browsing capabilities for a subset of organisms. You can view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. ...
... that provides special browsing capabilities for a subset of organisms. You can view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. ...
Supplementary Information Text
... additional three short exons that are alternatively cis-spliced to each and exon, providing a “constant” cytoplasmic region2-4. Each protocadherin gene is transcribed from its own promoter and all protocadherin cluster promoters share a highly conserved core motif5, 6. Promoter choice appears to ...
... additional three short exons that are alternatively cis-spliced to each and exon, providing a “constant” cytoplasmic region2-4. Each protocadherin gene is transcribed from its own promoter and all protocadherin cluster promoters share a highly conserved core motif5, 6. Promoter choice appears to ...
DNA Paper Model Activity Try to attach and mode the Gene Reading
... 2. Refer to question 1, would this be an active or inactive gene? Explain. It’s inactive, because the methyl groups make the DNA inaccessible. 3. Try to attach and move the Gene Reading Machinery cut-out to any length of the accessible DNA ribbon that is not spooled around a histone or covered by a ...
... 2. Refer to question 1, would this be an active or inactive gene? Explain. It’s inactive, because the methyl groups make the DNA inaccessible. 3. Try to attach and move the Gene Reading Machinery cut-out to any length of the accessible DNA ribbon that is not spooled around a histone or covered by a ...
Human Genome Project and Cloning and
... cell and then took a mammary cell from an adult sheep and fused them together using electric shock. The egg was then placed into a surrogate mother or substitute mother so that the egg could develop. ...
... cell and then took a mammary cell from an adult sheep and fused them together using electric shock. The egg was then placed into a surrogate mother or substitute mother so that the egg could develop. ...
Using DNA Subway in the Classroom Red Line Lesson
... First, use DNA subway to show how we can reveal features of a sequence. Create a project using a sample sequence. Once students have mastery, they can come back and create their own projects using real data. ...
... First, use DNA subway to show how we can reveal features of a sequence. Create a project using a sample sequence. Once students have mastery, they can come back and create their own projects using real data. ...
Lecture 5
... 1) the majority of DNA in the human genome is transcribed into functional molecules RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along ...
... 1) the majority of DNA in the human genome is transcribed into functional molecules RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along ...
1 Forward and Reverse Genetics 1. Background What is the function
... a) X-rays - cause breaks in double-stranded DNA, resulting in large deletions of pieces of chromosome or chromosomal re-arrangements. These mutations are typically easy to map by cytological examination of chromosomes, but are often not limited to single genes. Not good for fine-scale mutagenesis. b ...
... a) X-rays - cause breaks in double-stranded DNA, resulting in large deletions of pieces of chromosome or chromosomal re-arrangements. These mutations are typically easy to map by cytological examination of chromosomes, but are often not limited to single genes. Not good for fine-scale mutagenesis. b ...
Part 1: Prokaryotic Regulation Questions to answer
... they similar? How are they different? What determines if an operon will be repressible or inducible? Give an example of each type of operon in a typical prokaryotic cell. Explain the function of the CAP/cAMP system. Why is it necessary? ...
... they similar? How are they different? What determines if an operon will be repressible or inducible? Give an example of each type of operon in a typical prokaryotic cell. Explain the function of the CAP/cAMP system. Why is it necessary? ...
TOC - G3: Genes | Genomes | Genetics
... Raquel da Cunha, Elsa Lauwers, Mark Fiers, and Patrik Verstreken Genome editing is a powerful method to study gene function. In this work, Vilain and Vanhauwaert et al. present a novel genome editing methodology for fruit flies based on MiMIC transposons that are present throughout the genome. The me ...
... Raquel da Cunha, Elsa Lauwers, Mark Fiers, and Patrik Verstreken Genome editing is a powerful method to study gene function. In this work, Vilain and Vanhauwaert et al. present a novel genome editing methodology for fruit flies based on MiMIC transposons that are present throughout the genome. The me ...
Document
... Align and match homologous gene sequences in databases and seek to determine function. ...
... Align and match homologous gene sequences in databases and seek to determine function. ...
What are 3 major limitations of using the chimpanzee genome for
... This exam consists of four sets of questions relating to the four indicated papers that have appeared in the past few months. Each question is worth 5 points, for a total of 100 points. You should write up to a half page for each answer. ...
... This exam consists of four sets of questions relating to the four indicated papers that have appeared in the past few months. Each question is worth 5 points, for a total of 100 points. You should write up to a half page for each answer. ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.