Homework #4
--Retrieving DNA sequence/GenBank-- | ||
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1.Sho-Hua cloned a gene in the lab. The DNA sequence is listed here:A A T T A A T T C T C T C A A T C A A A T C C A A T T T T C T C C C T A T A A A A A C C C T A A G G T C C T A T A G T G T T C T A T A T C C A A C A C T A G C T C C T A C T C C C T A A A G C A T T T A T T A T A T C T T C C C C T G T G T T C T A T A T C C A A C A C T A G C T C C T A C T C C C T A A A G C A T T T A T T A T A T C T T C C C C T A G C T A G A T A C T T C A T T C C A C A A A T A G T T T G C A G C T T T T T C T T T T C C T C T A A A A C A A T G G A A A T A G C T G G G A A A A T T G C A T G C T T T G T G G T A T T G T G C A T G G T G G T A G C T G C A C C C T G C G C A G A A G C C A T A A C C T G T G G C C A G G T T A C G T C G A A T T T G G C A C C T T G T C T T G C T T A T C T T A G A A A C A C G G G G C C T C T G G G A C G T T G T T G C G G T G G C G T T A A G G C T C T G G T G A A T T C T G C A A G G A C C A C A G A A G A T C G T C A A A T T G C A T G C A C T T G C C T G A A A T C A G C T G C A G G T G C T A T T T C T G G A A T C A A T T T G G G C A A A G C T G C T G G T C T C C C T A G T A C T T G T G G T G T C A A T A T T C C T T A C A A G A T C A G C C C T T C C A C T G A C T G C T C C A A G T A C C T C A C T T T T T T T C T C T C T C A T G C T A T T C T T A T C C T T A T A T T C T A T C T G C T T C A T T T T C G C T T A T C T T T T A A A T T T T T T A T T C G G A A T C T T T A T A C C A Please help him to identify the gene and its protein sequence. |
Use NCBI-BLAST to find out the results.
LOCUS: NTLTP1 312 bp DNA PLN 18-NOV-1996
REFERENCE1 (bases 1 to 3112)
AUTHORS Kuhlemeier,C.
TITLE Direct Submission
JOURNAL Submitted(19-DEC-1991)C.Kuhlemeier, Institute of
Plant Physiology, Altenbergrain 21, Ch-3013 Bern,
SWITZERLAND
REFERENCE2(bases 1038 to 3112)
AUTHORS Fleming,A.J.,Mandel,T.,Hofmann,S.,Sterk,P.,
de Vries,S.C. and Kuhlemeier,C.
TITLE Expression pattern of a tobacco lipid transfer
protein gene within the shoot apex
JOURNAL Plant J. 2 (6), 855-862 (1992)
REFERENCE3 (bases 1 to 3112)
AUTHORS Caderas,D.
TITLE Direct Submission
JOURNAL Submitted(18-NOV-1996)D.Caderas, Institute of
Plant Physiology,University of Berne,
Altenbergrain 21, CH-3013 Berne, SWITZERLAND
REFERENCE4 (bases 1 to 3112)
AUTHORS Canevascini,S.,Caderas,D.,Mandel,T.,Fleming,A.J.,
Dupuis,I. and Kuhlemeier,C.
TITLE Tissue-specific expression and promoter analysis of
the tobacco Itp1 gene
JOURNAL Plant Physiol. 112 (2), 513-524 (1996)
FEATURES:Location/Qualifiers
source 1..3112
/organism="Nicotiana tabacum"
/cultivar="Samsun"
/db_xref="taxon:4097"
/dev_stage="leaf"
/clone_lib="lambda EMBL3"
sig_peptide 1347..1415
/gene="Ltp1"
CDS join(1347..1681,2662..2671)
/gene="Ltp1"
/codon_start=1
/product="lipid transferase"
/db_xref="PID:g19883"
/translation="MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLA
YLRNTGPLGRCCGGVKALVNSARTTEDRQIACTCLKSAA
GAISGINLGKAAGLPSTCGVNIPYKISPSTDCSKVQ"
prim_transcript <1347..>2671
/gene="Ltp1"
exon <1347..1681
/gene="Ltp1"
/number=1
gene 1347..2671
/gene="Ltp1"
mat_peptide join(1416..1681,2662,1680..1681,2662..2668)
/gene="Ltp1"
/product="lipid transferase"
intron 1682..2661
/gene="Ltp1"
/number=1
exon 2662..>2671
/gene="Ltp1"
/number=2 PLN 18-NOV-1996
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2.How many nucleotide and protein sequence of Lycopersicon esculentum were know? Please find its class II small heat shock protein mRNA, complete cds. |
Use NCBI-Anotomy to find 817 nts. and 1092 proteins
known for Lycopersicon esculentum (common tomato) till 12.8,1997.
LOCUS: LEU72396 738 bp-mRNA PLN 14-JAN-1997
REFERENCE1 (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)
REFERENCE2 (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
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