Assignment 3: Finding out more about your gene of interest. This assignment is similar to
Assignment 2, except that I would like you to answer some questions about your gene of
interest. You can use NCBI and Swiss-Prot for this exercise. You have created a basic page for
your gene in the Web with some links. This assignment will collect some of the information
about YG on your web page, which will come in handy.
1. Start in the “Gene” Database at NCBI. You can get there from the NCBI homepage. Put a link to
YG (your gene) on the home page.
Answer:
Site has been posted to MT Gene Webpage:
General link: http://www.ncbi.nlm.nih.gov/sites/gquery
Specific Gene Interest:
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=4489
&ordinalpos=9&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum
2. Find the RefSeq for YG’s cDNA and Protein. How many nucleotides are in the cDNA and how
many amino acids are in the protein. Put a link on your homepage
***Used MT1A for Homo sapiens reference
Nucleotide Reference: NM_005946
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005946.2
# of nucleotides in cDNA: 468 bp
Protein Reference: NP_005937
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_005937.2
# of amino acids in protein: 61 aa
3. What Chromosome is YG on? Which chromosome arm is it on? How many nucleotides are listed
in this entire chromosome? How many introns does YG have? Put a link to the MapViewer for YG.
Put in a link to the complete human chromosome sequence that your gene is on.
Location on Chromosome: 16q13
# of nucleotides on entire chromosome:
# of introns: 2
HBA2 (162875..163708)
HBA1 (166679..167520)
Link to the complete human chromosome sequence:
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=16&query=uid(739572,12721674
)&QSTR=4489%5Bgene%5Fid%5D&maps=gene_set&cmd=focus
4. Are there functional protein domains described for YG? Give a link for YG that discusses its
domains.
5. Can you find any PubMed references for this gene? Give me some link(s) to a PubMed search you
performed to learn more about YG.
References:
Reference 1:
Sutherland DE, Stillman MJ. Noncooperative cadmium(II) binding to human metallothionein 1a.
Biochem Biophys Res Commun. 2008 Aug 8;372(4):840-4. Epub 2008 Jun 3. PMID: 18533113
[PubMed - indexed for MEDLINE]
Reference 2:
Rigby Duncan KE, Kirby CW, Stillman MJ. Metal exchange in metallothioneins: a novel structurally
significant Cd(5) species in the alpha domain of human metallothionein 1a. FEBS J. 2008
May;275(9):2227-39. PMID: 18429853 [PubMed - indexed for MEDLINE]
Reference 3:
Thirumoorthy N, Manisenthil Kumar KT, Shyam Sundar A, Panayappan L, Chatterjee M.
Metallothionein: an overview. World J Gastroenterol. 2007 Feb 21;13(7):993-6. Review. PMID:
17373731 [PubMed - indexed for MEDLINE]
6. Does this gene have any homologs in other species? Give me some links to some of them. You can
find this through Homologene Database.
Homologs in other species:
HomoloGene:81614. Gene conserved in Eutheria
HomoloGene:4346. Gene conserved in Amniota
HomoloGene:48388. Gene conserved in Euteleostomi
HomoloGene:98181. Gene conserved in Magnoliophyta
7. YG is in OMIM. What is a biological consequence of a mutation in this protein for humans? Give
me the OMIM link on your page.
OMIM link:
http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=156350
8. Can you find your gene in SwissProt (http://us.expasy.org/sprot/) database ? Give me the accession
number in SwissProt.