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Thread: Genetics - Nucleotide sequencing and using NCBI?

  1. #1 Genetics - Nucleotide sequencing and using NCBI? 
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    Hi,
    Ok, so i'm new to bioinformatics and don't really know what im doing!

    I am doing an assignment on tumor protein 53 and have been using the NCBI website and at the moment im stuck on a question.

    For the information below, I am supposed to find the nucleotide sequences of the gene (which is the sequences under the origin heading yes?) and the amino acid sequence data which I have been told is under the Features heading, though I have no idea how to read the information given! Any ideas?


    FEATURES Location/Qualifiers
    source 1..2331
    /organism="Homo sapiens"
    /mol_type="mRNA"
    /db_xref="taxon:9606"
    /chromosome="17"
    /map="17p13.1"
    gene 1..2331
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /note="tumor protein p53"
    /db_xref="GeneID:7157"
    /db_xref="HGNC:11998"
    /db_xref="MIM:191170"
    exon 1..441
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=5a
    STS 243..558
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="GDB:178567"
    /db_xref="UniSTS:155019"
    STS 243..486
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="GDB:363689"
    /db_xref="UniSTS:156784"
    STS 243..353
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="GDB:177724"
    /db_xref="UniSTS:154952"
    CDS 279..923
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /note="isoform f is encoded by transcript variant 7; p53
    tumor suppressor; phosphoprotein p53; p53 antigen; p53
    transformation suppressor; transformation-related protein
    53"
    /codon_start=1
    /product="tumor protein p53 isoform f"
    /protein_id="NP_001119589.1"
    /db_xref="GI:187830909"
    /db_xref="GeneID:7157"
    /db_xref="HGNC:11998"
    /db_xref="MIM:191170"
    /translation="MFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHM TEVVRRC
    PHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVG SDCTTIHY
    NYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRT EEENLRKK
    GEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFL INSS"
    STS 360..434
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="PMC340938P3"
    /db_xref="UniSTS:273171"
    exon 442..554
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=6
    exon 555..664
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=7
    STS 635..833
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="PMC310707P2"
    /db_xref="UniSTS:272633"
    STS 639..713
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="GDB:190076"
    /db_xref="UniSTS:155620"
    exon 665..801
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=8
    exon 802..875
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=9
    exon 876..935
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=10b
    exon 936..1042
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=11
    exon 1043..2331
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /inference="alignment:Splign"
    /number=12
    STS 1194..1310
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="D17S1678"
    /db_xref="UniSTS:82485"
    STS 1651..1797
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="D17S1506E"
    /db_xref="UniSTS:151711"
    STS 2186..2262
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    /standard_name="WI-20715"
    /db_xref="UniSTS:59997"
    polyA_signal 2295..2300
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    polyA_site 2312
    /gene="TP53"
    /gene_synonym="FLJ92943; LFS1; p53; TRP53"
    ORIGIN
    1 tgaggccagg agatggaggc tgcagtgagc tgtgatcaca ccactgtgct ccagcctgag
    61 tgacagagca agaccctatc tcaaaaaaaa aaaaaaaaaa gaaaagctcc tgaggtgtag
    121 acgccaactc tctctagctc gctagtgggt tgcaggaggt gcttacgcat gtttgtttct
    181 ttgctgccgt cttccagttg ctttatctgt tcacttgtgc cctgactttc aactctgtct
    241 ccttcctctt cctacagtac tcccctgccc tcaacaagat gttttgccaa ctggccaaga
    301 cctgccctgt gcagctgtgg gttgattcca cacccccgcc cggcacccgc gtccgcgcca
    361 tggccatcta caagcagtca cagcacatga cggaggttgt gaggcgctgc ccccaccatg
    421 agcgctgctc agatagcgat ggtctggccc ctcctcagca tcttatccga gtggaaggaa
    481 atttgcgtgt ggagtatttg gatgacagaa acacttttcg acatagtgtg gtggtgccct
    541 atgagccgcc tgaggttggc tctgactgta ccaccatcca ctacaactac atgtgtaaca
    601 gttcctgcat gggcggcatg aaccggaggc ccatcctcac catcatcaca ctggaagact
    661 ccagtggtaa tctactggga cggaacagct ttgaggtgcg tgtttgtgcc tgtcctggga
    721 gagaccggcg cacagaggaa gagaatctcc gcaagaaagg ggagcctcac cacgagctgc
    781 ccccagggag cactaagcga gcactgccca acaacaccag ctcctctccc cagccaaaga
    841 agaaaccact ggatggagaa tatttcaccc ttcagatgct acttgactta cgatggtgtt
    901 acttcctgat aaactcgtcg taagttgaaa atattatccg tgggcgtgag cgcttcgaga
    961 tgttccgaga gctgaatgag gccttggaac tcaaggatgc ccaggctggg aaggagccag
    1021 gggggagcag ggctcactcc agccacctga agtccaaaaa gggtcagtct acctcccgcc
    1081 ataaaaaact catgttcaag acagaagggc ctgactcaga ctgacattct ccacttcttg
    1141 ttccccactg acagcctccc acccccatct ctccctcccc tgccattttg ggttttgggt
    1201 ctttgaaccc ttgcttgcaa taggtgtgcg tcagaagcac ccaggacttc catttgcttt
    1261 gtcccggggc tccactgaac aagttggcct gcactggtgt tttgttgtgg ggaggaggat
    1321 ggggagtagg acataccagc ttagatttta aggtttttac tgtgagggat gtttgggaga
    1381 tgtaagaaat gttcttgcag ttaagggtta gtttacaatc agccacattc taggtagggg
    1441 cccacttcac cgtactaacc agggaagctg tccctcactg ttgaattttc tctaacttca
    1501 aggcccatat ctgtgaaatg ctggcatttg cacctacctc acagagtgca ttgtgagggt
    1561 taatgaaata atgtacatct ggccttgaaa ccacctttta ttacatgggg tctagaactt
    1621 gacccccttg agggtgcttg ttccctctcc ctgttggtcg gtgggttggt agtttctaca
    1681 gttgggcagc tggttaggta gagggagttg tcaagtctct gctggcccag ccaaaccctg
    1741 tctgacaacc tcttggtgaa ccttagtacc taaaaggaaa tctcacccca tcccacaccc
    1801 tggaggattt catctcttgt atatgatgat ctggatccac caagacttgt tttatgctca
    1861 gggtcaattt cttttttctt tttttttttt ttttttcttt ttctttgaga ctgggtctcg
    1921 ctttgttgcc caggctggag tggagtggcg tgatcttggc ttactgcagc ctttgcctcc
    1981 ccggctcgag cagtcctgcc tcagcctccg gagtagctgg gaccacaggt tcatgccacc
    2041 atggccagcc aacttttgca tgttttgtag agatggggtc tcacagtgtt gcccaggctg
    2101 gtctcaaact cctgggctca ggcgatccac ctgtctcagc ctcccagagt gctgggatta
    2161 caattgtgag ccaccacgtc cagctggaag ggtcaacatc ttttacattc tgcaagcaca
    2221 tctgcatttt caccccaccc ttcccctcct tctccctttt tatatcccat ttttatatcg
    2281 atctcttatt ttacaataaa actttgctgc cacctgtgtg tctgaggggt g



    Then i'm supposed to mark sites of initiation and termination on the nucleotide sequence. I know the initiation codon is atg, so does that mean whenever I find atg in the sequence it is an initiation site?

    For example in this line, is the place ive put the (()) around an initiation site?
    1 tgaggccagg ag((atg))gaggc tgcagtgagc tgtgatcaca ccactgtgct ccagcctgag

    How many initiation and termination sites should there be?

    I'm so confused! Hopefully someone can set me straight, I tried talking to my lecturer but he isnt very good with english and has a hard time explaining. I've been trying to learn this course from a text book and can only get so far.

    Thanks!


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  3. #2  
    Moderator Moderator TheBiologista's Avatar
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    The protein sequence is under the heading "translation":

    MFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERC SDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVG SDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCA CPGRDRRT EEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLL DLRWCYFLINSS

    The nucleotide sequence does indeed start under "origin" with the number 1. The start codon is usually atg (transcribed as "aug" in RNA) which encodes the first methionine (M) in the protein sequence above.


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  4. #3  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Another interesting fact is that p53 is like spinach. Spinach is a superfood. P53 is a super molecule.

    Why is it a supermolecule? It does everything! You can't think of a single function or process it hasn't been associated with.

    Terribly wonderful.
    "Kill them all and let God sort them out."

    - Arnaud Amalric

    http://spuriousforums.com/index.php
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  5. #4  
    Moderator Moderator TheBiologista's Avatar
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    Quote Originally Posted by spuriousmonkey
    Another interesting fact is that p53 is like spinach. Spinach is a superfood. P53 is a super molecule.

    Why is it a supermolecule? It does everything! You can't think of a single function or process it hasn't been associated with.

    Terribly wonderful.
    Ah, it's a great little macromolecule to be sure. If P53 were a piece of plastic cutlery, it'd be some sort of omni-spork.
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  6. #5  
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    Haha an omni-spork? I doubt my lecturer would appreciate me comparing p53 to plastic cutlery in my assignment! Shame.

    :-D

    Anyway, Thanks for your help! I think I have it sorted now.
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