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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtctgtgaaacaaagtaataatatcttttacttgggtagtttactttttgtgctgctattctgatttttccatattatttttttcttcttcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCTGAGCTGCTTACTCAAACAGCTGGTTTCTCTTCTGCTGAAATACAAGATG

Basic information

species Vitis vinifera
transcript Vv16s0050g01460.t01
intron # 9
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|30297567|gb|CB974361.1|CB974361
EST:     TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAG                         AAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT
genomic: TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAGgtaactagaa ... tcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT
EST: gi|161720446|gb|FC070213.1|FC070213
EST:     TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAG                         AAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT
genomic: TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAGgtaactagaa ... tcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT
EST: gi|29782441|gb|CB347748.2|CB347748
EST:     TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAG                         AAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT
genomic: TGCAGTTGCCGCATTTCAGTGAGGCTATTATAAAAAAGATAGCCCGTAAGgtaactagaa ... tcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtgctgctattctgatttttccatattatttttttcttcttcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCTGAGCTGCTTACTCAAACAGCTGGTTTCTCTTCTGCTGAAATACAAGATG
              ttctgat  putative branch site (score: 3)
                    tttttccatattattt  CT-rich tract
            tattctgatttttcca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtctgtgaaacaaagtaataatatcttttacttgggtagtttactttttgtgctgctattctgatttttccatattatttttttcttcttcatttgcagAAAGTGCGGACATTTCAGGAGCTCTCAGACATGCCCCTGCAGGAGCGTGCTGAGCTGCTTACTCAAACAGCTGGTTTCTCTTCTGCTGAAATACAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - aaacaaa
- - - - - - - - - - - - - - -tacttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctat