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2008 Spring Biological database Homework 1
9680560 林儀潤
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?
ii.
What database(s) did you search, and what tool(s) did you use in your search?
What parameter settings did you use?
Answer: NCBIMap viewrKey in EPO.
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.
Answer:
mRNA sequence :
>gi|55742714|ref|NM_214134.1| Sus scrofa erythropoietin (EPO), mRNA
GCAGCCCCCTCCTTAGGGCGGAGAGGTGGCCCTGTCCCGCCAGGCTTTCCAGGATGCGGGCTCCCGGCGC
CGGCACCCGCCAAGCCCCAGGACGCTGAGGGGCCGGGCGAGGCGCGGAGATGGGGGCGCGCGAATGTCCT
GCCCGGCTGCTTCTGCTGTCCTTGCTGCTGCTTCCTCTGGGCCTCCCAGTCCTGGGCGCCCCCCCACGCC
TCATCTGTGACAGCCGAGTCCTGGAGAGGTACATCTTGGAGGCCAAGGAGGGCGAAAATGCCACGATGGG
CTGTGCCGAAAGCTGCAGCTTCAGTGAGAATATCACTGTCCCAGACACCAAGGTTAACTTCTATGCCTGG
AAGAGGATGGAGGTCCAGCAGCAGGCCATGGAGGTCTGGCAGGGTCTGGCCCTGCTCTCAGAAGCCATCC
TGCAGGGCCAGGCCCTGTTGGCCAACTCCTCCCAGCCATCTGAGGCCCTGCAGCTGCATGTGGACAAAGC
TGTCAGCGGCCTGCGCAGCCTCACCTCCCTGCTTCGGGCGCTGGGAGCCCAGAAGGAAGCCATCCCCCTT
CCAGACGCATCCCCCTCCTCTGCCACCCCACTCCGAACATTTGCTGTTGATACTTTGTGCAAACTTTTCC
GCAACTACTCCAATTTCCTGCGGGGAAAGCTGACGCTGTACACTGGAGAGGCCTGCAGGAGAAGGGACAG
GTGACTTGGTGCTCCCACCCGGGGCATGTCCACCACTTCGCTCACCACCACTGCCTGTGCCATGCCTTCT
GCACCTCCACTCCCAACCCCCGCTGAGGGGCCATCAGCTCAGCGCCAGCCTGTCCCATGGACACTCCAGG
GCCAGCGGTGACATCTCAAGGGCTAAAGGAACCGTCCAGAGCTCAACTCAAACCTAAGGATGTCACGGGG
CCAGCCTGAGCCCCCAAAGCAGGAGGAATTCAGAGATCAGCTTAAACTTGGGGACAGTGCCAGTCTGGGG
AGACAGTGAGACTCATCTTGGCGCCCTGCACAACTGTGATGCCTGGACAAGCTGGAGGGAAAATACCTCC
TTCTGCACCTACCAAGCAGGGACAGAATGGACTGGAGAATTTAGGAGGCAAGCCATGAATTCTCCAGGTC
TCATGGAGACTCCCACAACAGCAAGAGCCCACTGGACAAGGAGGGTGGTGGGAGCCCGTGACGGGATGGG
GGCTGGCCCCCTGGCTCTCACTAGGTCCAAGTTTTGTGTATTTTTCAATCTCACTGGCAAGAACTGAAAC
CAC
Protein sequence:
>gi|55742715|ref|NP_999299.1| erythropoietin [Sus scrofa]
MGARECPARLLLLSLLLLPLGLPVLGAPPRLICDSRVLERYILEAKEGENATMGCAESCSFSENITVPDT
KVNFYAWKRMEVQQQAMEVWQGLALLSEAILQGQALLANSSQPSEALQLHVDKAVSGLRSLTSLLRALGA
QKEAIPLPDASPSSATPLRTFAVDTLCKLFRNYSNFLRGKLTLYTGEACRRRDR
The similarity of mRNA sequence between Homo sapiens and Sus scrofa is
82%. And the similarity of protein sequence is 77&.
iv.
Retrieve at least 5 homologenes of this gene. Perform a multiple sequence
alignment? The human sequence is most similar to what organism?
Answer:
The Pan trogloedytes is most similar to Homo sapines.
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?
Answer:
There are four helical folds in EPO.
Key in ERYTHROPOIETIN Sequence detail .
vi.
Is the function of this protein known? If so, what does it do?
Answer:
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?
Answer : The major tissue is prostate.
Map viewer Key in EPOUnigeneExpression profile.
viii. Is this protein involved in any biological pathway(s)? If so, what does the
pathway do?
Answer: EPO is involved in cytokine-cytokine interaction, hematopoietic cascades,
JAK-STAT pathway.
viiii. Do any other databases contain information about the superfamily of this target
gene product? Which superfamily? How did you find out?
Answer: EPO-TPO superfamily.
GeneCardEPOProtein domain families.
ix.
Look for publications relevant to the function(s) of this protein in the biomedical
literature. Show one abstract of a relevant article.
Differential regulation of the IL-17 receptor by gamma c cytokines:Inhibitory
signaling by the PI 3'-kinase pathway.
Lindemann MJ, Hu Z, Benczik M, Liu KD, Gaffen SL.
Oral Biology, University at Buffalo, State University of New York, Buffalo, NY
14214.
The gammac-family cytokine IL-2 activates signaling events that contribute to cell
survival and proliferation, the best-studied of which are the STAT-5 and PI3K
pathways. The starting point of this study was to define genes regulated by the
IL-2R-mediated PI3K pathway in T cells. Accordingly, we used an erythropoietin
(EPO) receptor chimeric receptor system in which IL-2-dependent HT-2 T cells
expressed a mutant EPO-IL-2Rbeta construct where Tyr-338 is mutated to Phe.
Cells expressing this mutant IL-2Rbeta chain fail to induce phosphorylation of
PI3K-p85alpha/beta or activate Akt, but mediate normal IL-2-dependent
proliferation and activation of JAK1 and STAT-5A/B. Microarray analyses
revealed differential regulation of numerous genes compared to cells expressing a
wild type IL-2Rbeta, including upregulation of the IL-17 receptor subunit IL-17RA.
Blockade of the PI3K pathway but not p70S6K led to up-regulation of IL-17RA,
and constitutive Akt activation was associated with suppressed IL-17RA
expression. Moreover, similar to the mutant EPO-IL-2Rss chimera, IL-15 and
IL-21 induced IL-17RA preferentially compared to IL-2, and IL-2 but not IL-15 or
IL-21 mediated prolonged activation of the PI3K p85 regulatory subunit. Thus,
there are intrinsic signaling differences between IL-2 and IL-15 that can be
attributed to differences in activation of the PI3K pathway.
x.
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?
Answer: EPO gene of human is located on chromosome 7.
And EPO gene of zebra fish is located on chromosome 3 and 7.
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 zebrafish? How did you determine
this?
Answer: There are five exons in EPO sequence of zebra fish.
NCBIMAP viewr ev.
iv.
What is the expression pattern of this gene in zebrafish? In human? In mouse?
Answer:
Expression patterns in zebra fish are EPO family.
In human is EPO/TPO family.
In mouse are erythropoietin, dynein, thrombopoietin.