Find 5'Utr Ahead Of A Gene In Chromosome

Question

[Sarbesh]

AGGGGTGTGCAGGTTTGTGTTTGTGCGTGGCGCGTCCGCCATG

This is a part of Nucleotide Sequence from OsSUT1 gene. I want to know sequences ahead of this sequences (about180 nucloetides). I found the chromosome from BLAST search but it is too large. How do I match my sequence?

Thanks

Answer 1

[Pierre Lindenbaum]

The blast returns the following hit:

>dbj|AB551389.1|  Oryza sativa Indica Group OsSUT1 gene for sucrose transporter, 
complete cds, cultivar: Milyang 23
Length=6794


                                                         Sort alignments for this subject sequence by:
                                                           E value  Score  Percent identity
                                                           Query start position  Subject start position
 Score = 85.7 bits (43),  Expect = 3e-16
 Identities = 43/43 (100%), Gaps = 0/43 (0%)
 Strand=Plus/Plus

Query  1    AGGGGTGTGCAGGTTTGTGTTTGTGCGTGGCGCGTCCGCCATG  43
            |||||||||||||||||||||||||||||||||||||||||||
Sbjct  597  AGGGGTGTGCAGGTTTGTGTTTGTGCGTGGCGCGTCCGCCATG  639


 Score = 24.3 bits (12),  Expect =   903
 Identities = 12/12 (100%), Gaps = 0/12 (0%)
 Strand=Plus/Minus

Query  12   GGTTTGTGTTTG  23
            ||||||||||||
Sbjct  449  GGTTTGTGTTTG  438

It links to: http://www.ncbi.nlm.nih.gov/nucleotide/291461617 from 597 to 639

select "change region shown" to 397 597

LOCUS       AB551389                 201 bp    DNA     linear   PLN 24-MAR-2010
DEFINITION  Oryza sativa Indica Group OsSUT1 gene for sucrose transporter,
            complete cds, cultivar: Milyang 23.
ACCESSION   AB551389 REGION: 397..597
VERSION     AB551389.1  GI:291461617
KEYWORDS    .
SOURCE      Oryza sativa Indica Group
  ORGANISM  Oryza sativa Indica Group
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
            clade; Ehrhartoideae; Oryzeae; Oryza.
REFERENCE   1
  AUTHORS   Kato,T. and Horibata,A.
  TITLE     Rice Sucrose Transporter 1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 201)
  AUTHORS   Kato,T. and Horibata,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAR-2010) Contact:Tsuneo Kato Kinki University,
            Faculty of Biology-Oriented Science and Technology; 930
            Nishimitani, Kinokawa, Wakayama 649-6493, Japan
FEATURES             Location/Qualifiers
     source          1..201
                     /organism="Oryza sativa Indica Group"
                     /mol_type="genomic DNA"
                     /cultivar="Milyang 23"
                     /db_xref="taxon:39946"
                     /chromosome="3"
ORIGIN      
        1 ctccctccct ttaaatgctt cgcctctctc gctcgtctct ccaaacacaa acccaccacc
       61 tcctcctcct cctcccatcc agcacgcgcc tcctctctcg cgcggctttc catttccatc
      121 tccccctcct cctcctacgt ctccgccgct cctcacttcc tccactcgat ttcctttctt
      181 ggcctctcct cctctgacac a

Answer 2

[JC]

You can use Gramene ( http://www.gramene.org/Multi/blastview?species=Oryza_sativa ), blating your sequence I found the same hit with a nice plot:

http://www.gramene.org/Oryza_sativa/Location/View?r=3:3800928-3804970;h=BLAST_NEW:BLA_UmcXgrE8V!!20111018

From here you can explore the gene context.