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2008 Spring Biological database Homework 1
This problem set is due by 2PM, March 25, 2008. You shall upload your answers to your web site as instructed by your
TA. For all questions, please make a reference such as screen-shot to indicate the source of your answer.
1. Here is a nucleotide sequence:
CTCCAGGCCCGTGGGGCTGGCCCTGCACCGCCGAGCTTCCCGGGATGAGGGCCCCCGGTGTGGTCACCCG
GCGCGCCCCAGGTCGCTGAGGGACCCCGGCCAGGCGCGGAGATGGGGGTGCACGAATGTCCTGCCTGGCT
GTGGCTTCTCCTGTCCCTGCTGTCGCTCCCTCTGGGCCTCCCAGTCCTGGGCGCCCCACCACGCCTCATC
TGTGACAGCCGAGTCCTGGAGAGGTACCTCTTGGAGGCCAAGGAGGCCGAGAATATCACGACGGGCTGTG
CTGAACACTGCAGCTTGAATGAGAATATCACTGTCCCAGACACCAAAGTTAATTTCTATGCCTGGAAGAG
GATGGAGGTCGGGCAGCAGGCCGTAGAAGTCTGGCAGGGCCTGGCCCTGCTGTCGGAAGCTGTCCTGCGG
GGCCAGGCCCTGTTGGTCAACTCTTCCCAGCCGTGGGAGCCCCTGCAGCTGCATGTGGATAAAGCCGTCA
GTGGCCTTCGCAGCCTCACCACTCTGCTTCGGGCTCTGGGAGCCCAGAAGGAAGCCATCTCCCCTCCAGA
TGCGGCCTCAGCTGCTCCACTCCGAACAATCACTGCTGACACTTTCCGCAAACTCTTCCGAGTCTACTCC
AATTTCCTCCGGGGAAAGCTGAAGCTGTACACAGGGGAGGCCTGCAGGACAGGGGACAGATGACCAGGTG
TGTCCACCTGGGCATATCCACCACCTCCCTCACCAACATTGCTTGTGCCACACCCTCCCCCGCCACTCCT
GAACCCCGTCGAGGGGCTCTCAGCTCAGCGCCAGCCTGTCCCATGGACACTCCAGTGCCAGCAATGACAT
CTCAGGGGCCAGAGGAACTGTCCAGAGAGCAACTCTGAGATCTAAGGATGTCACAGGGCCAACTTGAGGG
CCCAGAGCAGGAAGCATTCAGAGAGCAGCTTTAAACTCAGGGACAGAGCCATGCTGGGAAGACGCCTGAG
CTCACTCGGCACCCTGCAAAATTTGATGCCAGGACACGCTTTGGAGGCGATTTACCTGTTTTCGCACCTA
CCATCAGGGACAGGATGACCTGGAGAACTTAGGTGGCAAGCTGTGACTTCTCCAGGTCTCACGGGCATGG
Please use database mining tools of your choice to tell me as much as you can about this
sequence.
i.
What gene does this sequence represent in human? What is its GI number? GenBank
Accession number? Gene symbol? Unigene ID?
Ans: Homo sapiens erythropoietin (EPO)
Ans: Gi=62240996
Ans: accession number=NM_000799
Ans: gene symbol=EPO ; UGID=131206
ii.
What database(s) did you search, and what tool(s) did you use in your search? What parameter
settings did you use?
Ans: NCBI/NCBI BLAST/nucleotide blast→FASTA format→Human
genome plus transcripts→BLAST
iii.
Retrieve one ortholog of this gene’s complete mRNA sequence and Protein sequence in
FASTA format. Compare the results obtained by blastn vs. blastp.
I used Genecards database to find the orthologues of human EPO, and I
chose “Dog orthologue” to answer this question.
The dog’s EPO mRNA FASTA sequence retrieved from NCBI.
The dog’s EPO protein FASTA sequence retrieved from NCBI.
The result of BLASTP
The result of BLASTN
Ans:
BLASTN: Search a nucleotide database using a nucleotide query.
BLASTP: Search protein database using a protein query.
iv.
Retrieve at least 5 homologenes of this gene. Perform a multiple sequence alignment? The
human sequence is most similar to what organism?
I used NCBI HomoloGene database to find EPO homologenes.
Download the homologene file.
used the homologene file to do Multi alignment.
Ans: The human sequence is most similar to Common Chimpanzee (Pan
troglodytes).
v.
Is the secondary structure of this protein known? If so, how many “helical fold”are there in its
3D protein structure? How did you determine the exact amino acid number of each helical
region?
Ans: YES. There are four helical folds in 3D structure.
Ans: PDB→sequence details.
vi.
Is the function of this protein known? If so, what does it do?
Ans: Yes. erythropoietin is the principal hormone involved in the
regulation of erythrocyte differentiation and the maintenance of a
physiological level of circulating erythrocyte mass.
vii.
Which normal human tissues is this gene mainly expressed in? How did you determine this?
Ans: eye、prostate. NCBI Unigene→epo expression profile.
viii.
Is this protein involved in any biological pathway(s)? If so, what does the pathway do?
Ans: Yes. JAK-STAT signaling pathway.
ix.
Do any other databases contain information about the superfamily of this target gene product?
Which superfamily? How did you find out?
Ans: Yes. 4-helical cytokines superfamily. I used the PDB database.
x.
Look for publications relevant to the function(s) of this protein in the biomedical literature.
Show one abstract of a relevant article.
xi.
Show the protein 3-D structure if there is any.
1. Find the zebra fish homolog of the above gene. And answer the following questions:
i.
The zebra fish homolog is located on which chromosome? And in Human?
Ans: Chromosome 7
Ans: Chromosome 7
ii.
Perform a cDNA and Polypeptide sequence alignment between human and zebra fish of this
gene.
This is cDNA sequence alignment of EPO between human and
zebrafish.
This is polypeptide sequence alignment of EPO between human and
zebrafish.
iii.
How many exons does this gene have in zebrafish? How did you determine this?
Ans: 5 exons. I used Ensambl database→exon information.
iv.
What is the expression pattern of this gene in zebrafish? In human? In mouse?
Zebrafish EPO
Human EPO
There is no expression profile about EPO in mouse.