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?
Homo sapiens erythropoietin
GI:62240996
NM_000799
EPO
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?
Ncbi
fasta
Entrez gene
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.
blastn
>gi|62240996|ref|NM_000799.2| Homo sapiens erythropoietin (EPO), mRNA
CCCGGAGCCGGACCGGGGCCACCGCGCCCGCTCTGCTCCGACACCGCGCCCCCTGGACAGCCGCCCTCTC
CTCCAGGCCCGTGGGGCTGGCCCTGCACCGCCGAGCTTCCCGGGATGAGGGCCCCCGGTGTGGTCACCCG
GCGCGCCCCAGGTCGCTGAGGGACCCCGGCCAGGCGCGGAGATGGGGGTGCACGAATGTCCTGCCTGGCT
GTGGCTTCTCCTGTCCCTGCTGTCGCTCCCTCTGGGCCTCCCAGTCCTGGGCGCCCCACCACGCCTCATC
TGTGACAGCCGAGTCCTGGAGAGGTACCTCTTGGAGGCCAAGGAGGCCGAGAATATCACGACGGGCTGTG
CTGAACACTGCAGCTTGAATGAGAATATCACTGTCCCAGACACCAAAGTTAATTTCTATGCCTGGAAGAG
GATGGAGGTCGGGCAGCAGGCCGTAGAAGTCTGGCAGGGCCTGGCCCTGCTGTCGGAAGCTGTCCTGCGG
GGCCAGGCCCTGTTGGTCAACTCTTCCCAGCCGTGGGAGCCCCTGCAGCTGCATGTGGATAAAGCCGTCA
GTGGCCTTCGCAGCCTCACCACTCTGCTTCGGGCTCTGGGAGCCCAGAAGGAAGCCATCTCCCCTCCAGA
TGCGGCCTCAGCTGCTCCACTCCGAACAATCACTGCTGACACTTTCCGCAAACTCTTCCGAGTCTACTCC
AATTTCCTCCGGGGAAAGCTGAAGCTGTACACAGGGGAGGCCTGCAGGACAGGGGACAGATGACCAGGTG
TGTCCACCTGGGCATATCCACCACCTCCCTCACCAACATTGCTTGTGCCACACCCTCCCCCGCCACTCCT
GAACCCCGTCGAGGGGCTCTCAGCTCAGCGCCAGCCTGTCCCATGGACACTCCAGTGCCAGCAATGACAT
CTCAGGGGCCAGAGGAACTGTCCAGAGAGCAACTCTGAGATCTAAGGATGTCACAGGGCCAACTTGAGGG
CCCAGAGCAGGAAGCATTCAGAGAGCAGCTTTAAACTCAGGGACAGAGCCATGCTGGGAAGACGCCTGAG
CTCACTCGGCACCCTGCAAAATTTGATGCCAGGACACGCTTTGGAGGCGATTTACCTGTTTTCGCACCTA
CCATCAGGGACAGGATGACCTGGAGAACTTAGGTGGCAAGCTGTGACTTCTCCAGGTCTCACGGGCATGG
GCACTCCCTTGGTGGCAAGAGCCCCCTTGACACCGGGGTGGTGGGAACCATGAAGACAGGATGGGGGCTG
GCCTCTGGCTCTCATGGGGTCCAAGTTTTGTGTATTCTTCAACCTCATTGACAAGAACTGAAACCACCAA
AAAAAAAAAA
>gi|62240997|ref|NP_000790.2| erythropoietin precursor [Homo sapiens]
MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPD
TKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLRSLTTLLRALG
AQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR
Blastp
>gi|118911371|gb|ABL56459.1| Sequence 367 from patent US 7141547
MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPD
TKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLRSLTTLLRALG
AQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDDAHKSEVAHRFKDLGEEN
FKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMA
DCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFA
KRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEF
AEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEM
PADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHE
CYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCC
KHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFT
FHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAA
SQAALGL
iv.
Retrieve at least 5 homologenes of this gene. Perform a multiple sequence
alignment? The human sequence is most similar to what organism?
From ensemble
Danio rerio
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
4
vi.
Is the function of this protein known? If so, what does it do?
vii.
Which normal human tissues is this gene mainly expressed in? How did you
determine this?
prostate
From nabi
viii.
Is this protein involved in any biological pathway(s)? If so, what does the
pathway do?
ix.
Do any other databases contain information about the superfamily of this
target gene product? Which superfamily? How did you find out?
4-helical cytokines
From PDB
x.
Look for publications relevant to the function(s) of this protein in the
biomedical literature. Show one abstract of a relevant article.
Erythropoietin (EPO) promotes neuronal survival after hypoxia and other metabolic insults by largely unknown mechanisms.
Apoptosis and necrosis have been proposed as mechanisms of cellular demise, and either could be the target of actions of
EPO. This study evaluates whether antiapoptotic mechanisms can account for the neuroprotective actions of EPO. Systemic
administration of EPO (5,000 units/kg of body weight, i.p.) after middle-cerebral artery occlusion in rats dramatically
reduces the volume of infarction 24 h later, in concert with an almost complete reduction in the number of terminal
deoxynucleotidyltransferase-mediated dUTP nick-end labeling of neurons within the ischemic penumbra. In both pure and
mixed neuronal cultures, EPO (0.1--10 units/ml) also inhibits apoptosis induced by serum deprivation or kainic acid
exposure. Protection requires pretreatment, consistent with the induction of a gene expression program, and is sustained for 3
days without the continued presence of EPO. EPO (0.3 units/ml) also protects hippocampal neurons against hypoxia-induced
neuronal death through activation of extracellular signal-regulated kinases and protein kinase Akt-1/protein kinase B. The
action of EPO is not limited to directly promoting cell survival, as EPO is trophic but not mitogenic in cultured neuronal
cells. These data suggest that inhibition of neuronal apoptosis underlies short latency protective effects of EPO after cerebral
ischemia and other brain injuries. The neurotrophic actions suggest there may be longer-latency effects as well. Evaluation of
EPO, a compound established as clinically safe, as neuroprotective therapy in acute brain injury is further supported.
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:
Uni gene
epo
i.
The zebra fish homolog is located on which chromosome? And in Human?
zebra fish :7
Human :7
ii.
Perform a cDNA and Polypeptide sequence alignment between human and
zebra fish of this gene.
Unigene for erythropoietin
D. rerio
Protein sequence
>gi|125821250|ref|XP_001337902.1| PREDICTED: similar to erythropoietin isoform 2
[Danio rerio]
MFHGSGLFALLLMVLEWTRPGLSSPLRPICDLRVLDHFIKEAWDAEAAMRTCKDDCSIATNVTVPLTRVD
FEVWEAMNIEEQAQEVQSGLHMLNEAIGSLQISNQTEVLQSHIDASIRNIASIRQVLRSLSIPEYVPPTS
SGEDKETQKISSISELFQVHVNFLRGKARLLLANAPVCRQGVS
>gi|125821249|ref|XM_001337866.1| PREDICTED: Danio rerio similar to erythropoietin, transcript variant 2
(LOC100004455), mRNA
GCCTCTCACTGAGTTCTTGGAAGCAGCGCGTAGGGCTTGATGCGTCTGTGCTCCAGTCCATCCATGTCTT
TTGTGCCACAAGTTGAGCTGTTTTTGCGCGCGATTTGTCATTTTTAATCATGTGTTTGAAAAATGCCAAG
TTGTTTTGCGAATGTTTCACGGTTCAGGACTCTTTGCCTTACTGCTGATGGTGCTGGAGTGGACCCGTCC
AGGCCTGTCCTCCCCATTACGCCCCATCTGTGACCTGCGCGTCCTCGACCATTTCATTAAGGAGGCATGG
GATGCAGAGGCTGCTATGAGAACTTGTAAGGACGATTGCAGCATTGCAACGAACGTCACTGTTCCTCTGA
CCAGAGTCGATTTTGAAGTCTGGGAAGCGATGAATATAGAGGAGCAAGCTCAGGAGGTCCAGTCAGGCTT
ACACATGCTGAACGAGGCCATTGGCTCATTACAGATATCTAATCAGACTGAAGTGCTTCAGTCTCACATA
GATGCCAGTATTAGAAACATCGCCAGCATCAGACAAGTGCTGCGAAGTCTCAGCATACCGGAATATGTAC
CTCCAACCAGTAGTGGAGAAGACAAGGAGACACAGAAAATATCCTCGATCTCAGAGCTGTTTCAGGTCCA
TGTCAACTTTCTTCGGGGAAAAGCGCGTCTGCTGCTCGCCAATGCACCTGTCTGTCGACAGGGTGTCAGC
TGA
Human
>gi|62240997|ref|NP_000790.2| erythropoietin precursor [Homo sapiens]
MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPD
TKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLRSLTTLLRALG
AQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR
>gi|62240996|ref|NM_000799.2| Homo sapiens erythropoietin (EPO), mRNA
CCCGGAGCCGGACCGGGGCCACCGCGCCCGCTCTGCTCCGACACCGCGCCCCCTGGACAGCCGCCCTCTC
CTCCAGGCCCGTGGGGCTGGCCCTGCACCGCCGAGCTTCCCGGGATGAGGGCCCCCGGTGTGGTCACCCG
GCGCGCCCCAGGTCGCTGAGGGACCCCGGCCAGGCGCGGAGATGGGGGTGCACGAATGTCCTGCCTGGCT
GTGGCTTCTCCTGTCCCTGCTGTCGCTCCCTCTGGGCCTCCCAGTCCTGGGCGCCCCACCACGCCTCATC
TGTGACAGCCGAGTCCTGGAGAGGTACCTCTTGGAGGCCAAGGAGGCCGAGAATATCACGACGGGCTGTG
CTGAACACTGCAGCTTGAATGAGAATATCACTGTCCCAGACACCAAAGTTAATTTCTATGCCTGGAAGAG
GATGGAGGTCGGGCAGCAGGCCGTAGAAGTCTGGCAGGGCCTGGCCCTGCTGTCGGAAGCTGTCCTGCGG
GGCCAGGCCCTGTTGGTCAACTCTTCCCAGCCGTGGGAGCCCCTGCAGCTGCATGTGGATAAAGCCGTCA
GTGGCCTTCGCAGCCTCACCACTCTGCTTCGGGCTCTGGGAGCCCAGAAGGAAGCCATCTCCCCTCCAGA
TGCGGCCTCAGCTGCTCCACTCCGAACAATCACTGCTGACACTTTCCGCAAACTCTTCCGAGTCTACTCC
AATTTCCTCCGGGGAAAGCTGAAGCTGTACACAGGGGAGGCCTGCAGGACAGGGGACAGATGACCAGGTG
TGTCCACCTGGGCATATCCACCACCTCCCTCACCAACATTGCTTGTGCCACACCCTCCCCCGCCACTCCT
GAACCCCGTCGAGGGGCTCTCAGCTCAGCGCCAGCCTGTCCCATGGACACTCCAGTGCCAGCAATGACAT
CTCAGGGGCCAGAGGAACTGTCCAGAGAGCAACTCTGAGATCTAAGGATGTCACAGGGCCAACTTGAGGG
CCCAGAGCAGGAAGCATTCAGAGAGCAGCTTTAAACTCAGGGACAGAGCCATGCTGGGAAGACGCCTGAG
CTCACTCGGCACCCTGCAAAATTTGATGCCAGGACACGCTTTGGAGGCGATTTACCTGTTTTCGCACCTA
CCATCAGGGACAGGATGACCTGGAGAACTTAGGTGGCAAGCTGTGACTTCTCCAGGTCTCACGGGCATGG
GCACTCCCTTGGTGGCAAGAGCCCCCTTGACACCGGGGTGGTGGGAACCATGAAGACAGGATGGGGGCTG
GCCTCTGGCTCTCATGGGGTCCAAGTTTTGTGTATTCTTCAACCTCATTGACAAGAACTGAAACCACCAA
AAAAAAAAAA
Protein sequence alignment
Score = 92.8 bits (229), Expect = 2e-17
Identities = 59/161 (36%), Positives = 90/161 (55%), Gaps = 10/161 (6%)
Nucleotide sequence alignment
No significant similarity was found
iii.
How many exons does this gene have in zebrafish? How did you determine
this?
5
iv.
What is the expression pattern of this gene in zebrafish? In human? In mouse?
Human
Mouse
zebrafish