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?
由這個網頁可以知道，此序列為 Homo sapiens erythropoietin (EPO)、
GI:62240996、GenBank Accession number NM_000799
由這個網頁可以知道 Gene symbol 為 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?
使用 NCBI 的 BLAST，並選擇 nucleotide blast，設定為 human genomic+transcript
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.
黑猩猩(Pan troglodytes) mRNA
>gi|114615072|ref|XM_519268.2| PREDICTED: Pan troglodytes erythropoietin (EPO), mRNA
CCCGGAGCCGGAACGGGGCCACCGCGCCCGCTCTGCTCCGACACCGCGCCCCCTGGACAGCCGCCCTCTC
CTCCAGGCCCGTGGGGCTGGCCCTGCACCGCCGAGCTTCCCGGGATGAGGGCCCCCGGTGTGGTCACCCG
GCGCGCCCCAGGTCGCTGAGGGACCCCGGCCAGGCGCGGAGATGGGGGTGCACGAATGTCCTGCCTGGCT
GTGGCTTCTCCTGTCCCTGCTGTCGCTCCCTCTGGGCCTCCCAGTCCTGGGCGCCCCACCACGCCTCATC
TGTGACAGCCGAGTCCTGGAGAGGTACCTCTTGGAGGCCAAGGAGGCCGAGAATATCACGACGGGCTGTG
CCGAACACTGCAGCTTGAATGAGAATATCACTGTCCCAGACACCAAAGTTAATTTCTATGCCTGGAAGAG
GATGGAGGTCAGGCAGCAGGCCGTAGAAGTCTGGCAGGGCCTGGCCCTGCTCTCGGAAGCTGTCCTGCGG
GGCCAGGCCCTGTTGGTCAACTCTTCCCAGCCGTGGGAGCCCCTGCAGCTGCATGTGGATAAAGCCGTCA
GTGGCCTTCGCAGCCTCACCACTCTGCTTCGGGCTCTGGGAGCCCAGAAGGAAGCCATCTCCCCTCCAGA
TGCGGCCTCAGCTGCTCCACTCCGAACAATCACTGCTGACACTTTCCGCAAACTCTTCCGAGTCTACTCC
AATTTCCTCCGGGGAAAGCTGAAGCTGTACACAGGGGAGGCCTGCAGGACAGGGGACAGATGACCAGGTG
TGTCCACCTGGGCATATCCACCACCTCCCTCACCAACATTGCTTGTGCCACACCCTCCCCCGCCACTCCT
GAACCCCGTCGAGGAGCTCTCAGCTCAGCGCCAGCCTGTCCCTTGGACACTCCAGTGCCAGCAATGACAT
CTCAGGGGCCAGAGAAACTGTCCAGAGAGCAACTCTGAGATCTAAGGATGTCACAGGGCCAACTTGAGGG
CCCAGAGCAGGAAGCATTCAGAGAGCAGCTTTAAACTCAGGGACAGAGCCATGCTGGGAAGACGCCTGAG
CTCACTCGGCACCCTGCAAAATTTGATGCCAGGACACGCTTTGGAGGCGATTTACCTGTTTTCGCACCTA
CCATCAGGGACAGGATGACCTGGAGAACTTAGGTGGCAAGCTGTGACTTCTCCAGGTCTCACGGGCATGG
GCACTCCCTTGGTGGCAAGAGCCCCCTTGACACCGGGGTGGTGGGAACCATGAAGACAGGATGGGGGCTG
GCCTCTGGCTCTCATGGGGTCCAAGTTTTATGTATTCTTCAATCTCATTGACAAGAACTGAAACCACCAA
→黑猩猩(Pan troglodytes)與人類 EPO mRNA 的比較
黑猩猩(Pan troglodytes)的 protein sequence
>gi|114615073|ref|XP_519268.2| PREDICTED: erythropoietin [Pan troglodytes]
MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPD
TKVNFYAWKRMEVRQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLR
SLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR
→黑猩猩(Pan troglodytes)與人類 EPO protein 的比較
iv.
Retrieve at least 5 homologenes of this gene. Perform a multiple sequence
alignment? The human sequence is most similar to what organism?
由此網站可知道與人類最相似的是黑猩猩(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?
There are four helical fold
vi.
Is the function of this protein known? If so, what does it do?
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?
再人類的表現處有十二個，Bone marrow, Spleen, Thymus, Brain, Spinal Cordially,
Heart, Skeletal muscle, Liver, Pancreas, Prostate, Kiney, lung
viii.
Is this protein involved in any biological pathway(s)? If so, what does the
pathway do?
EPO Signaling Pathway
Erythropoietin mediated neuroprotection through NF-kB
Visceral Fat Deposits and the Metabolic Syndrome
ix.
Do any other databases contain information about the superfamily of this
target gene product? Which superfamily? How did you find out?
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.
Idebenone showed minimal benefit on MMF-related diarrhea and anemia. BM of
MMF-treated rats revealed erythroid aplasia as a possible reason for anemia. Marked
upregulation of EPO-mRNA presumably reflects a compensatory mechanism. Because
ROS have the potential to suppress EPO expression, it can be hypothesized that
enhanced EPO-mRNA expression in MMF/idebenone-treated rats is caused by
antagonism of ROS.
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?
在第 7 chromosome
主要也是在第 7 chromosome
ii.
Perform a cDNA and Polypeptide sequence alignment between human and
zebra fish of this gene.
cDNA sequence alignment→
Polypeptide sequence alignment→
iii.
How many exons does this gene have in zebrafish? How did you determine
this?
有 5 exon
iv.
What is the expression pattern of this gene in zebrafish? In human? In mouse?
in zebrafish
In human
In mouse