Lecture 1 exercises

• BIOF518

DNA

Novice

• Which chromosome is mindbomb1 (Dm) on?
  1. Search all NCBI databases for mindbomb1
  2. Find that official symbol is mib1
  3. In NCBI Gene database for Drosophila melanogaster, we see gene lies on chromosome 3L
• How many SNPs does its human homolog have?
  1. From NCBI Gene page, click on "Holologs of the mib1 gene
  2. Arrive at NCBI HomoloGene DB for MIB1, click on Homo Sapiens
  3. From list of links at right, click on SNP
  4. Takes you to NCBI dbSNP. We see it lists 1786 for active.
  5. Could also go straight to dbSNP and type mib1 AND homo sapiens
• How many of them would change the protein translated from it?
  1. Go to Ensembl and look for mib1 in human
  2. Click on the Gene result
  3. At the top, click on the "Gene: MIB1" tab
  4. In the navigation on the left, click "Variation table" inder Genetic Variation
  5. If you click on ALL we see that Ensembl lists 81 total variations, and 70 of them are attributed to SNPs
  6. Brute force: You can also download the variations from dbSNP and write a perl script to go to each variation and see if the polymorphism changes the encoded protein

Advanced

• What is the sequence (10 bp) 500 bp upstream from TTN
  • in human?
  • in drosophila?
• Obtain unique identifiers (UIs) for all genes associated with FSHD
• Find ENSGs for them

RNA

Novice

• What are the last 10 nt in the human homolog of mindbomb1?
  1. Search NCBI Nucleotide mib1 and homo spaiens
  2. Click on "Homo sapiens mindbomb homolog 1 (Drosophila) (MIB1), mRNA"
  3. At the very bottom they give the nucleotide sequence:

     9241 aaatttcatg gcaatatttt ttactaaatt gaaactatag gttttaaaaa taaagacatt
     9301 ttagaaaa

• How many exons would you hypothesize the RNA would have if the last amino acid is a lysine?
  • Not sure. I see that looking for the MIB1 homosapiens in NCBI Nucleotide that there are 20 exons listed there.
• How does expression of this gene change in CD4+ T-cells in patients with melanoma?
• Would upregulation of mindbomb1 have any effect on the number of mitochondrial ribosomes?

Advanced

• What is the titin isoform with the largest # of exons?
• Find a transcription factor that upregulates the expression of this mRNA
• Find a microRNA that could suppress it (has >= 14/21 matches)
• Find the exons for all mouse 3’UTRs (don’t download them, just show me the first MB)
• Verify your terminal-K hypothesis

Protein

Novice

• How many glutamines are there in the human homolog of mindbomb protein?
  1. Look up "mib1 and homo sapiens" in NCBI protein
  2. Copy the protein sequence at the bottom, beside the word "ORIGIN"
  3. Use the following perl subroutine to identify the number of glutamines (letter q) in the sequence

sub count_qs {
	my $sequence = shift;

	my $count = 0;

	print "length: " . length($sequence). "\n";

	for (my $key = 0; $key < length($sequence); $key++)
	{
		my $letter = substr ($sequence, $key, 1);
		#print $letter;
		if ($letter eq 'q' )
		{
			$count++;
		}
	}
	print $count . "\n";
}

• 1. Answer: 54
• Name a protein that binds (h)MIB1.
• How many ankyrin repeats does (h)MIB1 have?
  • By clicking on the "Graphics" link on the NCBI Protein page, we see that there are several areas labelled ANK. In the chart, it looks like there are 9 separable regions with ANK, each labelled 1-9.
• Name another protein with ankyrin repeats.
  • According to Ankyrin Repeat wiki article, many proteins have ankyrin repeats, including NOTCH1.
• Which kingdom of life has the most ankyrin repeats?
  • According to same article, eukaryotes have the most.

Advanced

• How many aliphatic amino acids does an ankyrin repeat consensus sequence contain?
• What is the pdb identifier of the homologous region to MIB1 on Ank1?
• How many isoforms of Ank1 have this region?
• How many do not?
• Download all predicted proteins in brachiostoma floridiae
• How many domains does the largest isoform of titin have?