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NCBI, GENE BANK

 


GenBank Overview:


Learn how to navigate NCBI GenBank with the following video:



Activity 1: Retrieve the correct type of biological data from a given database.

Go to - https://www.ncbi.nlm.nih.gov/gene/60. Search for “gene” “ACTB”. This is the human beta-actin gene. Click on the GenBank link that will take you to the sequence of this gene. Learn the annotations here. Start of the gene, end of the gene, mRNA, and CDS, and the difference between them. Also, have a look at the expression pattern.


Assignment: Generate a report that will include -


ACTB gene sequence, ACTB mRNA sequence, CDS sequence, and protein sequence. Please answer the following question in your report -

How would you explain similarities and differences observed within these sequences?

Repeat the same process for the human Insulin gene and include the same information for the human insulin gene in your report.


Activity 2: Characterizing Data

In this activity, you will characterize the genomic data from NCBI GenBank. Go to https://www.ncbi.nlm.nih.gov/genbank/. Search for nucleotide sequences related to “human JUN”. Click on the very first hit which would read “Human c-jun proto-oncogene (JUN), complete cds, clone hCJ-1”. Note down the GenBank accession number.


Assignment: Answer the following questions in your report:


What chromosome is this gene located on?

How long is this gene?

Who has submitted this sequence to Genbank and when? In which year was their research published?

What cell type in humans did the researcher use to extract this gene sequence?

What is the coding sequence and protein sequence of this gene? How long is the protein and what is the GenBank accession number for the protein sequence?


Repeat the same process and create individual gene reports using the keywords:

Human MTR, human AKT3 and human NGF.


Activity 3: Sorting the given biological data to solve a biological question

Assignment: Find the DNA sequence for the human beta hemoglobin gene and answer the following questions:


What chromosome is this gene located on?

Would this gene make a protein?

In which tissues is this gene expressed?

What are some diseases/conditions associated with this gene?


Include your answers in the report you will submit at the end of this activity. The report is a project that you will work on:


Two different sequences are listed below. For each sequence, determine whether it is a DNA, RNA, or protein sequence and state whether they are the products of the human beta hemoglobin gene. To make that determination, you will need to remember the lesson/activity:


Sequence 1

AAUCACUGCUGUGCAGGGCAGGAAAGCUCCAUGCACAUAGCCCAGCAAAGAGCAACACAGAGCUGAAAGGAAGACUCAGAGGAGAGAGAUAAGUAAGGAAAGUAGUGAUGGCUCUCAUCCCAGACUUGGCCAUGGAAACC

Sequence 2 MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE

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