Homework4

  1. Ho to identify a gene and its protein sequence?

    We identify this sequence by BLASTof NCBI.And found N.tabacum ltp1 gene for lipid transferase is similar to query sequence with identity of 98%.

    Its protein sequence is following: 

      1  meiagkiacf vvlcmvvaap caeaitcgqv tsnlapclay
41  lrntgplgrc cggvkalvns arttedrqia ctclksaaga 
81  isginlgkaa glpstcgvni pykispstdc skvq

  2. How to get information from the name of an organism?

    By the help of Toxonomy of NCBI,we get almost all information about an organism just keying in its name. The following is an example of the searching result of class II small heat shock protein mRNA of Lycopersicon esculentum .

LOCUS       LEU72396      738 bp    mRNA            PLN       14-JAN-1997
DEFINITION  Lycopersicon esculentum class II small heat shock protein
            Le-HSP17.6 mRNA, complete cds.
ACCESSION   U72396
NID         g1773290
KEYWORDS    .
SOURCE      tomato.
  ORGANISM  Lycopersicon esculentum
            Eukaryotae; mitochondrial eukaryotes; Viridiplantae;
            Charophyta/Embryophyta group; Embryophyta; Magnoliophyta;
            Magnoliopsida; Solananae; Solanales; Solanaceae; Solanum clade;
            Lycopersicon.
REFERENCE   1  (bases 1 to 738)
  AUTHORS   Kadyrzhanova,D.K., Vlachonasios,K.E., Ververidis,P. and Dilley,D.R.
  TITLE     A heat-treatment chilling tolerance related cDNA from tomato fruit
            encoding a small heat-shock protein class II
  JOURNAL   Unpublished (1996)
REFERENCE   2  (bases 1 to 738)
  AUTHORS   Kadyrzhanova,D.K., Vlachonasios,K.E., Ververidis,P. and Dilley,D.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-SEP-1996) Horticulture, Michigan State University,
            Plant and Soil Science Building, East Lansing, MI 48824-1325, USA
FEATURES             Location/Qualifiers
     source          1..738
                     /organism="Lycopersicon esculentum"
                     /cultivar="Mountain Springs"
                     /db_xref="taxon:4081"
                     /clone_lib="tomato heat-shock/chilling tolerance lambda
                     gt11 library of D.R. Dilley"
                     /dev_stage="mature green fruit"
                     /tissue_type="pericarp"
                     /clone="pHCT1"
     CDS             108..584
                     /note="heat treatment/chilling tolerance related protein
                     from tomato fruit"
                     /codon_start=1
                     /product="class II small heat shock protein Le-HSP17.6"
                     /db_xref="PID:g1773291"
                     /translation="MDLRLLGIDNTPLFHTLHHMMEAAGEDSDKSVNAPSRNYVRDAK
                     AMAATPADVKEYPNSYVFVVDMPGLKSGDIKVQVEEDNVLLISGERKREEEKEGAKFI
                     RMERRVGKFMRKFSLPENANTDAISAVCQDGVLTVTVQKLPPPEPKKPKTIEVKVA"
     polyA_signal    629..634
BASE COUNT      229 a    117 c    183 g    209 t
ORIGIN      
        1 tacggctgcg agaagacgac agaaggggac tgcaattaca aatcaaacca aaattgacaa
       61 atttcacgca caaaatcaca atatccaaaa atttctcaat actgaaaatg gatttgaggt
      121 tgttgggtat cgataacaca ccactcttcc acactctcca ccatatgatg gaagctgccg
      181 gtgaagattc cgacaagtct gtcaatgcac catcaaggaa ctatgttcgt gatgctaagg
      241 ccatggctgc tacaccagcg gatgtgaagg agtatcctaa ttcgtatgtt tttgttgtgg
      301 atatgccagg gttgaaatct ggagatatca aagtgcaggt ggaagaagac aatgtgctgt
      361 tgattagtgg tgaaaggaag agggaagaag agaaagaagg tgcaaagttt attaggatgg
      421 agagaagggt tgggaaattc atgaggaagt ttagtctgcc agagaatgcg aatactgatg
      481 caatttctgc agtttgtcaa gatggagttc tgactgttac tgttcagaaa ttgcctcctc
      541 ctgagccaaa gaaacccaaa acaattgagg tgaaagttgc ttgaagttat ggactctgtt
      601 ttgatggttt gtggtatgat gtagtagaaa taaagttgta ggagtagtga acttttcctt
      661 tcatctttct gctatgtttt cacgtctgtt tgaatgttac aatagccatg ggtattgttt
      721 gttttgatgc caaaaaaa