Download 2008 Spring Biological database Homework 1

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?
From these websites, this gene is erythropoietin in human.
GI number is 62240996.
GenBank Accession number is NM_000799.
Gene symbol is EPO.
Unigene ID is Hs.2303.
ii.
What database(s) did you search, and what tool(s) did you use in your search?
What parameter settings did you use?
I use NCBI to search it.
BLAST and Map viewer.
I didn’t use any parameter setting.
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.
>gi|54792749|ref|NM_001006646.1| Canis lupus familiaris erythropoietin (EPO), mRNA
ATGTGTGAACCTGCCCCTCCAAAACCCACACAGTCAGCCTGGCACTCTTTTCCAGAATGTCCTGCCCTGC
TCCTTTTGCTGTCTTTGCTGCTGCTTCCTCTGGGCCTCCCAGTCCTGGGCGCCCCCCCTCGCCTCATTTG
TGACAGCCGGGTCCTGGAGAGATACATCCTGGAGGCCAGGGAGGCCGAAAATGTCACGATGGGCTGTGCT
CAAGGCTGCAGCTTCAGTGAGAATATCACCGTCCCAGACACCAAGGTTAATTTCTATACCTGGAAGAGGA
TGGATGTTGGGCAGCAGGCCTTGGAAGTCTGGCAGGGCCTGGCACTGCTCTCAGAAGCCATCCTGCGGGG
TCAGGCCCTGTTGGCCAACGCCTCCCAGCCATCTGAGACTCCGCAGCTGCATGTGGACAAAGCCGTCAGC
AGCCTGCGCAGCCTCACCTCTCTGCTTCGGGCGCTGGGAGCCCAGAAGGAGGCCATGTCCCTTCCAGAGG
AAGCCTCTCCTGCTCCACTCCGAACATTCACTGTTGATACTTTGTGCAAACTTTTCCGAATCTACTCCAA
TTTCCTCCGTGGAAAGCTGACACTGTACACAGGGGAGGCCTGCAGAAGAGGAGACAGGTGACCAGGTGCT
CCCACCCCAGGCACATCCACCACCTCACTCACTACCACTGCCTGGGCCACGCCTCTGCACCACCACTCCT
GACCCCTGTCCAGGGGTGATCTGCTCAGCACCAGCCTGTCCCTGTCCCTTGGACACTCCACGGCCAGTGG
TGATATCTCAAGGGCCAGAGGAACTGTCCAGAGCTCAAATCAGATCTAAGGATGTCACAGTGCCAGCCTG
AGGCCCGAAGCAGGAGGAATTCGGAGGAAATCAGCTCAAACTTGGGGACAGAGCCTTGCTCGGGAGACTC
ACCTCGGTGCCCTGCCGAACAGTGATGCCAGGACAAGCTGGAGGGCAATTGCCGATTTTTTGCACCTATC
AGGGAGAGACAGGAGAGGCTAGAGAACTAGGTGGCAAGCCATAAATCTTTTAGGCTTCGGGTCTCCTATG
ACAGCAAGAGCCCACTGGCAAAGGGGGGGGAGCCATGGAGATGGGATAGGGGCTGGCCCAAAAAAAAAAA
AA
>gi|54792750|ref|NP_001006647.1| erythropoietin [Canis lupus familiaris]
MCEPAPPKPTQSAWHSFPECPALLLLLSLLLLPLGLPVLGAPPRLICDSRVLERYILEAREAENVTMGCA
QGCSFSENITVPDTKVNFYTWKRMDVGQQALEVWQGLALLSEAILRGQALLANASQPSETPQLHVDKAVS
SLRSLTSLLRALGAQKEAMSLPEEASPAPLRTFTVDTLCKLFRIYSNFLRGKLTLYTGEACRRGDR
Blastn:
Blastp:
iv.
Retrieve at least 5 homologenes of this gene. Perform a multiple sequence
alignment? The human sequence is most similar to what organism?
Human erythropoietin is the most similar to 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?
Yes, the secondary structure of erythropoietin is known.
There are four helical folds in its 3D protein structure.
From these websites, I know the exact amino acid number of each helical
region. Helix 1 has 18 amino acids. Helix 2 has 28 amino acids. Helix 3 has
20 amino acids. Helix 4 has 24 amino acids.
vi.
Is the function of this protein known? If so, what does it do?
Yes.
This gene is a member of the EPO/TPO family and encodes a secreted,
glycosylated cytokine composed of four alpha helical bundles. The
protein is found in the plasma and regulates red cell production by
promoting erythroid differentiation and initiating hemoglobin synthesis.
This protein also has neuroprotective activity against a variety of
potential brain injuries and antiapoptotic functions in several tissue
types.
vii.
Which normal human tissues is this gene mainly expressed in? How did you
determine this?
Erythropoietin is mainly expressed in prostate from this website.
viii.
Is this protein involved in any biological pathway(s)? If so, what does the
pathway do?
Yes. Erythropoietin mediated neuroprotection through NF-kB.
ix.
Do any other databases contain information about the superfamily of this
target gene product? Which superfamily? How did you find out?
Yes, GeneCards contain information about the superfamily of erythropoietin.
Erythropoietin belongs to the EPO/TPO family.
x.
Look for publications relevant to the function(s) of this protein in the
biomedical literature. Show one abstract of a relevant article.
The aim of our study was to assess possible relations between prohepcidin,
iron status and inflammatory markers in hemodialysis (HD) patients, as well as
its association with resistance to recombinant human erythropoietin (rhEPO)
therapy. Fifty HD patients and 25 healthy controls were enrolled in the study.
Among HD patients, 25 were non-responders and 25 were responders to
rhEPO therapy. Complete blood cell count, reticulocyte count, and circulating
levels of ferritin, iron, transferrin saturation, C-reactive protein (CRP), soluble
interleukin (IL)-2 receptor (s-IL2R), soluble transferrin receptor (s-TfR), IL-6
and prohepcidin were measured in all patients and controls. HD patients
showed higher circulating levels of ferritin, s-TfR, CRP, IL-6, s-IL2R and
prohepcidin, and lower levels of transferrin compared to healthy controls.
Higher levels of s-TfR, CRP and lower levels prohepcidin were observed
among non-responders compared to responders. Prohepcidin levels
correlated negatively with s-TfR and reticulocyte count. The weekly rhEPO/kg
dose was found to be positively correlated with CRP, hemoglobin and s-TfR. In
conclusion, our data show that a close interaction exists between inflammation,
iron status and prohepcidin serum levels that ultimately regulate intracellular
iron availability. Prohepcidin and s-TfR, together with CRP, may prove to be
good markers of resistance to rhEPO therapy in HD patients.
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?
Erythropoietin is located on chromosome 7 in zebra fish.
Erythropoietin is located on chromosome 7 in human.
ii.
Perform a cDNA and Polypeptide sequence alignment between human and
zebra fish of this gene.
iii.
How many exons does this gene have in zebra fish? How did you determine
this?
Erythropoietin has 5 exons in zebra fish.
From Ensembl Genome Browser or NCBI (Map viewer), I can know it.
iv.
What is the expression pattern of this gene in zebra fish? In human? In mouse?
In zebra fish:
In human:
In mouse: