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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgtagcatatttcattcaaatatgttatgttcattcaaatatgttgtagtgtataaaggcagttgaagacattctatttggtcttttgatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGATCGCTTGGAGTTGCTGGTTGATAAAACTGCTAATATGCAAGGAAATACAT

Basic information

species Vitis vinifera
transcript Vv04s0008g05650.t01
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351043453|gb|FQ444053.1|FQ444053
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|30252438|gb|CB969989.1|CB969989
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|351034506|gb|FQ448182.1|FQ448182
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|161718558|gb|FC065383.1|FC065383
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCA-TGTCATGATAGAGA-TATTGATAAAGTTT-AGACAGAG-T-AT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|161715759|gb|FC066163.1|FC066163
EST:     ATGATCCCAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|27586637|gb|CB009332.1|CB009332
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|27584778|gb|CB007473.1|CB007473
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|351029819|gb|FQ427659.1|FQ427659
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|349808751|gb|FQ406601.1|FQ406601
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
EST: gi|110690970|gb|EE068536.1|EE068536
EST:     ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAG                         GTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT
genomic: ATGATCCAAATGCAGATAGGATAAACCGGTTAAAAGGTGAAATGGGTCAGgtgagttttt ... gatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtagtgtataaaggcagttgaagacattctatttggtcttttgatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGATCGCTTGGAGTTGCTGGTTGATAAAACTGCTAATATGCAAGGAAATACAT
                                         ttttgat  putative branch site (score: 4)
 tcttttg  CT-rich tract
 attctattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgtagcatatttcattcaaatatgttatgttcattcaaatatgttgtagtgtataaaggcagttgaagacattctatttggtcttttgatttgacagGTACGCAATGTCATGATAGAGAATATTGATAAAGTTTTAGACAGAGGTGATCGCTTGGAGTTGCTGGTTGATAAAACTGCTAATATGCAAGGAAATACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -tgtagca
- - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaca