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Arabidopsis Gene Project
GK-12 April Workshop
Karolyn Giang and Dr. Mulligan
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Reverse genetics
An approach used to determine the function of a gene from known DNA sequence
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BLAST: Basic Local Alignment Search Tool
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Gene project
You are working on an Arabidopsis gene discovery project, and your job is to sequence cDNAs and then learn all you can about the genes from all types of databases: DNA sequence, genome, and publication databases.
TCCTGCATTCAATGTGATCAATGGAGGCAGTCATGCTGGGAATAGTTTGGCTATGCAAGAGTTTATGATACTACCTGTAGGAGCTACCTCATTCTCGGAGGCCTTCCAGATGGGAAGTGAAGTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTG
Query sequence:
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1. What is the name of the gene that the
unknown cDNA sequence is derived from?
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1. What is the name of the gene that the
unknown cDNA sequence is derived from?
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1. What is the name of the gene that the unknown cDNA sequence is derived from?
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1. What is the name of the gene that the
unknown cDNA sequence is derived from? 2. Identify the location of this gene by Arabidopsis thaliana chromosome and genome locus.
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2. Identify the location of this gene by Arabidopsis thaliana chromosome and genome locus.
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3. What is the function of this gene?
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4. How many nucleotides are in the coding sequence of this gene?
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4. How many nucleotides are in the
coding sequence of this gene?
1434 nucleotides
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5. What sequence of amino acids is
encoded by your unknown cDNA sequence?
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6.In the Arabidopsis genome, what other gene has
the most similar protein sequence to your gene?
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6.In the Arabidopsis genome, what other gene has
the most similar protein sequence to your gene?
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6.In the Arabidopsis genome, what other gene has
the most similar protein sequence to your gene?
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7. In the human genome, what is the most
closely related gene to your Arabidopsis gene?
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7. In the human genome, what is the most closely related gene to your Arabidopsis gene?
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8. What T-DNA insertion for this gene
would be likely to knock out gene function?
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8. What T-DNA insertion for this gene
would be likely to knock out gene function?
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8. What T-DNA insertion for this gene
would be likely to knock out gene function?
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8. What T-DNA insertion for this gene
would be likely to knock out gene function?
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9.Give a literature citation to a research article that
studied a knock out of this gene in Arabidopsis.
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9.Give a literature citation to a research article that
studied a knock out of this gene in Arabidopsis.