Homework  7

   Jason Lee, a student in the department of Life Sciences,got the mRNA from

a plant. Here is the sequence:

   
        1 atccactact tcatcataaa cctcacaact actattctat cttctcttct ctaattttca
       61 taatcattaa gaatggaaat ggttaacaag attgcatgct ttgtgctttt atgcatggta
      121 gtggttgcac cccatgcaga ggcactaact tgtggtcaag ttacatctac cttggctcct
      181 tgtctccctt atctaatgaa tcgcggtcct ctcggaggct gttgtggtgg tgttaagggt
      241 cttttgggtc aagcccagac tacagtagac cgacagaccg catgcacttg cctaaaatca
      301 gctgcttctt cttttacagg ccttgatttg ggcaaagctg ctagtctccc tagcacttgt
      361 agtgtcaaca tcccttacaa gatcagcccc tctactgact gctctaaagt tcagtaaagc
      421 tgatcatcag aatttggttt catgaggaga attaagaata agatagatag cattgatctt
      481 gcttatggat cctttctttc tatgttgtat cagttgtcac tttctgtttt ttctgtgttt
      541 cctttaaatt ctcgtatgta gtcgagtctt gtatcgaaat ttgacgattg attatattgt
      601 atcagttgtt actttctgtt ttcctgtgtt tcttttaaaa tcgtatgtag tcgagtcttg
      661 tatcgaaatt tcccgattgg ctatgttgta ttaatctaat ctttgataat acacatctat
      721 cttatttggt

1. Please help him to translate the DNA sequence to protein sequence.

 MEMVNKIACF VLLCMVVVAP HAEALTCGQV TSTLAPCLPYLMNRGPLGGC
CGGVKGLLGQAQTTVDRQTA CTCLKSAASS FTGLDLGKAA SLPSTCSVNI PYKISPSTDCSKVQ
SEQUENCE   114 AA;  11716 MW; EA5981F6 CRC32.

2. Please help him to identify the complete cds of this gene.
    Use the graphic view to explain all the features of this gene.

gi|1519357 (U66466) lipid transfer protein 2 [Lycopersicon penne...
         1 gtaatccagc taagaacgtc agaagtaaaa caaacttgtc gtaaaatatt taatttgaag
       61 ttgtatttaa atcttaatta ttttttttta aagctatact cacatcattt caattattct
      121 ttttgtaaaa gtatctctag agcttcataa tttttttttt aaaaatcttc gatcaaactg
      181 ttagagtagg taaaagtctc acattgatgg ggaaatagac tgattatttg cttataagga
      241 tgtggacaat actcctctca tataatagca tttaagatta aattagacct aaataacata
      301 ttttagcatg atattagagt tatattcatt cttgtttgaa cttccgatcc acatctcaat
      361 tggatctaca taaaaaaggg atattaaagt aagtaaaagc cctacattaa tcgaggaatc
      421 tacttatacg aactttggtg ataaaaaaaa agactcctac acgtaagatg ttagaactag
      481 ctaccacatg actttagagc cagcataata atgtacacca tcaaaatgct ttaaattttc
      541 aacctaacaa ccaactacct ctctcactcc tccattggcc atctactcca aatttccctc
      601 tataaaaaca ctcaaccaaa acacatttct tctcatccac tacttcatca taaacctcac
      661 aactactatt ctatcttctc ttctctaatt ttcataatca ttaagaatgg aaatggttaa
      721 caagattgca tgctttgtgc ttttatgcat ggtagtggtt gcaccccatg cagaggcact
      781 aacttgtggt caagttacat ctaccttggc tccttgtctc ccttatctaa tgaatcgcgg
      841 tcctctcgga ggctgttgtg gtggtgttaa gggtcttttg ggtcaagccc agactacagt
      901 agaccgacag accgcatgca cttgcctaaa atcagctgct tcttctttta caggccttga
      961 tttgggcaaa gctgctagtc tccctagcac ttgtagtgtc aacatccctt acaagatcag
     1021 cccctctact gactgctcta agtatgttaa tttttcatct tttttgacct ataacaacac
     1081 ctaactcttc gtattaatcc tagtacgaaa aataaagtaa caaaaaaatg atatgtgcta
     1141 gcacattgtc acaatatgac atgcaagtgt gtttggtttt ctcaaaaaat aagtggattt
     1201 tttatttata ttttagtgtt aagaaatatt agtttaaaaa tatttatata tgtaattata
     1261 aagaaaaaag atactattat agttagtaca ttatgttttt gttatcatta tcattattat
     1321 tattattaat gttggttttg ttcattgtta atgcagagtt cagtaaagct gatcatcaga
     1381 atttggtttc atgaggagaa ttaagaataa gatagatagc attgatcttg cttatggatc
     1441 ctttctttct atgttgtatc agttgtcact ttctgttttt tctgtgtttc ctttaaattc
     1501 tcgtatgtag tcgagtcttg tatcgaaatt tgacgattga ttatattgta tcagttgtta
     1561 ctttctgttt tcctgtgttt cttttaaaat cgtatgtagt cgagtcttgt atcgaaattt
     1621 cccgattggc tatgttgtat taatctaatc tttgataata cacatctatc ttatttggta
     1681 tatgtactct ctcgtctatt caatattttt ggtctacttt tactagggtt tttttaatat
     1741 gcattacaca tatatatcaa attcgagtaa tatatagtat acgctattgt gtgctcattc
     1801 atctaggtac ctcctttttc taaccacttc ttacacgtac aatgctaatt attg

graphic view

3.After translation of this gene, please help him to do the protein sequence analysis
   (including  pI, mol. wt.,  secondary structure prediction, hydrophobic profile,
     homology search, prosite scanning..........)

1. Molecular weight: 11715.81
2. Theoretical pI: 8.36
3.  secondary structure prediction

4.  hydrophobic profile

5.homology search

6. prosite scanning

[1] PDOC00006PS00006 CK2_PHOSPHO_SITE
Casein kinase II phosphorylation site

Number of matches: 2
      1      63-66 TTVD
      2      82-85 TGLD

[2] PDOC00008PS00008 MYRISTYL
N-myristoylation site

Number of matches: 6
      1      28-33 GQVTST
      2      48-53 GGCCGG
      3      49-54 GCCGGV
      4      52-57 GGVKGL
      5      59-64 GQAQTT
      6      83-88 GLDLGK

[3] PDOC00516PS00597 PLANT_LTP
Plant lipid transfer proteins signature

            92-113 LPSTCSVNIPYKISPSTDCSKV