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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactctgaacatatttttgttagtttttttaaactctagacaacctccttaaattctgtgacaataatattttttcttatttttttcccctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGATGGGAAG

Basic information

species Vitis vinifera
transcript Vv08s0040g02540.t01
intron # 3
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|110363795|gb|EC927411.1|EC927411
EST:     TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCGAAG                         TTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
genomic: TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAGgtattgtttt ... ctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
EST: gi|30131639|gb|CB916978.1|CB916978
EST:     TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCGAAG                         TTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
genomic: TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAGgtattgtttt ... ctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
EST: gi|110382285|gb|EC939068.1|EC939068
EST:     TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCGAAG                         TTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
genomic: TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAGgtattgtttt ... ctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
EST: gi|110423955|gb|EC990308.1|EC990308
EST:     TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAG                         TTTTACACTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA
genomic: TGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAGgtattgtttt ... ctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttaaattctgtgacaataatattttttcttatttttttcccctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGATGGGAAG
                                           ccctaat  putative branch site (score: 3)
                       tattttttcttatttt  CT-rich tract
     taaattctgtgacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactctgaacatatttttgttagtttttttaaactctagacaacctccttaaattctgtgacaataatattttttcttatttttttcccctaatttcagTTTTACTCTGCACACTGGTGCTGGTCTAATTGTTCCTGAAATCCAAGATGATGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -ctctgaa
- - - - - - - - - - - - - - - - - - - - - - cctcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaataa