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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttcatgtgaaaatatcaaatttgcttctttgatttgcttccaatttgctaaatggttgcatat...

Basic information

species Vitis vinifera
transcript Vv02s0025g01580.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G43540.1 (Glycine max), 5'ss of exon 6
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttcatgtgaaaatatcaaatttgct--tctttgatttgcttccaatttgctaaatggttgcatat----------------------------------
|| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | |||||| | |||||| || || |||||| ||    ||       || | |   | |||  | || |  | | |||     |  |||| || |||||   |     |                                  
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgt-attattctaaagtt-ttctttatcttctat-------atttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G01940.3 (Glycine max), 5'ss of exon 6
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttcatgtgaaaat----atcaaatttgcttctttgat-ttgcttccaatttgctaaatggttgcatat--------------------------
|| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | |||||| |  ||||| ||||| |||||  ||    |||  ||   | ||  | |     | |  | ||   |  |||  |||     |||||    | ||||   || |                          
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAGgt-atcattctaaaatt-ttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttat--agtggtaaaattttattttaattttcatggtgtttacag

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G02690.2 (Glycine max), 5'ss of exon 6
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttc-atgtgaaaatatcaaatttgcttctttgatttgcttccaatttgctaaatggttgcatat
|| ||||||||||| |||||| ||||||| ||||||||||| ||||| || ||| | || ||     |  |  ||||||||   |||||  || || || |||     | ||   || |  |||     |   ||| |     | ||        |      ||  || ||  ||  || 
GTTCGTGATTACATTCATGTTCTTGATTTAGCAGATGGGCATATTGCTGCGTTGCGTAAACTGGATGATCCTAAAATAGgtatttattccaaatttattattttcttctaataatttactgtgttcttttggtaaactcttgacattagcaaatattgtgaatgtgaattgaatgatta-

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G36850.1 (Glycine max), 5'ss of exon 6
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaa--attgttctttgtccatgattggtttcatgtgaaaatatcaaatttgcttctttgatttgcttccaatttg--ctaaatggttgcatat
|| ||||||||||| |||||| ||||||| ||||||||||| ||||| || ||| | || ||     |  |  |||||||| | |||||  ||  ||| || | |    || | |   |   |         | || | ||    |   | ||  |   ||| ||   | |||| ||   |  
GTTCGTGATTACATTCATGTTCTTGATTTAGCAGATGGGCATATTGCGGCATTGCGTAAACTCAATGATCCTAAAATAGgt-attattcctaattattattttcttctaataacttactgtgttcttttg-gtaaactctggcattagcaattattgtgaatgtgaattgaatgattaatt--

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|27586173|gb|CB008868.1|CB008868
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110720449|gb|EE096391.1|EE096391
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAN                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110358293|gb|EC922402.1|EC922402
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110719820|gb|EE095280.1|EE095280
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCNGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110718272|gb|EE094913.1|EE094913
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGNGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110720256|gb|EE096017.1|EE096017
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCANAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCCGTTTTTGGAG
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTT-GGAG
EST: gi|110720916|gb|EE097257.1|EE097257
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTANCA-CTTGGGAACAGGAAAAGGAACATCGGTTTTGGAG
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTA-CAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAG
EST: gi|30329922|gb|CD013184.1|CD013184
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110718494|gb|EE095391.1|EE095391
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAN                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110720332|gb|EE096162.1|EE096162
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110385299|gb|EC949809.1|EC949809
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAATTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110718330|gb|EE095043.1|EE095043
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCANGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACANGAAGAGGAACATCCGTTTTGAAGA
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGA
EST: gi|110719030|gb|EE096543.1|EE096543
EST:     GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG                         GCTGTGAAGTGTACAACTTGGGAACAGGNAAAGGAAACATCGGTTT-GGAG
genomic: GGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattc ... ctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAA-CATCGGTTTTGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttcatgtgaaaatatcaaatttgcttctttgatttgcttccaatttgctaaatggttgcatat

- - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata