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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttctaagtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAACAAGAGCTCCAGCGAGCCCGCCAGCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g05170.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 7
gtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttcta-agtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAACAAGAGCTCCAGCGAGCCCGCCAGCAG
                                 |   | | |     | | | ||| | || ||      | ||  |    | | || | || | || ||   |      |||||  | | || |     ||| |||||  | | |  |     |      | |    ||||||||| ||| |      |   || ||||||||||||||||  | ||||  ||| || |||| |||||||||||||| || |||||||||||||| |||||||||
--------------------------------gtaaggccttttccgttaatttta-gatgaacttgtaaaattattgtgatataggttggtttgttgttcaatatgtcattattgagacccaataat-ttgtcatgttttatatatattt---tttgacttattttttaaatccctctttcta-----ttcattcagGCATATGTGCAACAATTAGAGAGCAGTAGGTTGAAACTGACCCAACTTGAGCAGGAGCTCCAGCGAGCACGCCAGCAG

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G28320.1 (Glycine max), 3'ss of exon 7
gtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttctaagtgttggatagtgtattttttggttatggt---ttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAACAAGAGCTCCAGCGAGCCCGCCAGCAG
                                 |   | | |   | | | | ||| | || ||      | ||  |  |   |   | |  || || ||   ||||     |||||  | | ||    |  | | |||||  | |||  |    |  | |  | |    ||||||| | ||| |      |   || ||||||||||||||||  | ||||  ||| || |||| |||||||||||||| || |||||||||||| | |||||||||
--------------------------------gtaaggccttttctgttaatttta-gatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaac-ttatcatgttttataaatatttctgaacttctttt---ttaaatccttgtttcta-----ttcattcagGCATATGTGCAACAATTAGAGAGCAGTAGGTTGAAACTGACCCAACTTGAGCAGGAGCTCCAGCGATCTCGCCAGCAG
















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|110359279|gb|EC920517.1|EC920517
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|71884309|gb|DT033364.1|DT033364
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|33409731|gb|CF215358.1|CF215358
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|110397602|gb|EC963367.1|EC963367
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTC
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTC
EST: gi|161710152|gb|FC061050.1|FC061050
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|71885133|gb|DT034188.1|DT034188
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|71888810|gb|DT037865.1|DT037865
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|71883209|gb|DT032264.1|DT032264
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
EST: gi|161720288|gb|FC070549.1|FC070549
EST:     GGCTTGCTCAAAATCGTGAAGCTGCCAGAATAAGCCGATTAAGGAAAAAG                         GCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctg ... ctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAACAAGAGCTCCAGCGAGCCCGCCAGCAG
                      cactaaa  putative branch site (score: 2)
                             tccctttttttggttt  CT-rich tract
                                 ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttctaagtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttagGCATATGTGCAACAGCTGGAGAATAGTCGGATGAAGCTGACCCAACTTGAACAAGAGCTCCAGCGAGCCCGCCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT