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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTTTCAGGTATAATAGACTCATTCGTGTACCATGGTCATAGGGCAATCAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttcag

Basic information

species Vitis vinifera
transcript Vv12s0178g00020.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0178g00020.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G36050.1 (Arabidopsis thaliana), 5'ss of exon 13
--------ACAGTTTCAGGTATAATAGACTCATTCGTGTACCATGGTCATAGGGCAATCAAGAAGAAGATGGAACTTGGGAAATTCAGCTGA-TTATTTGCCAATTGTGgtcattttcag----------------------------------------------------------
        ||||| || || ||||||||| | ||  | ||||||||||| |  || |||||||||||||||||| |||| ||||| |||| | |  |||     || | |   |||||                                                            
GTGTCTTCACAGTGTCCGGGATAATAGACGCGTTTATATACCATGGTCAAAAAGCTATCAAGAAGAAGATGGAAATTGgtaaatttagctaaatcctttaagcctttttggggttttcgtctctctctttttgttttgcggataatacgattcatgctccaaatgtaatatggtgtca
















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|30137944|gb|CB923282.1|CB923282
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|30137944|gb|CB923282.1|CB923282
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|71890676|gb|DT039731.1|DT039731
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|71890676|gb|DT039731.1|DT039731
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|110357757|gb|EC921480.1|EC921480
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|110357757|gb|EC921480.1|EC921480
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|30130137|gb|CB915476.1|CB915476
EST:     AGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGG                         TCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTC
genomic: AGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGT-Ggtcattttca ... tcattttcagTCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTC
EST: gi|32271127|gb|CD720286.1|CD720286
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|32271127|gb|CD720286.1|CD720286
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|30296234|gb|CB973028.1|CB973028
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|30296234|gb|CB973028.1|CB973028
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|110363519|gb|EC927113.1|EC927113
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|110363519|gb|EC927113.1|EC927113
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|110395365|gb|EC961027.1|EC961027
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGG                         TCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTA
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGT-Ggtcattttca ... tcattttcagTCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTC
EST: gi|34362104|gb|CF403689.1|CF403689
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|34362104|gb|CF403689.1|CF403689
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|32461194|gb|CD802368.1|CD802368
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGG                         TCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTA
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGT-Ggtcattttca ... tcattttcagTCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTC
EST: gi|30328230|gb|CD011492.1|CD011492
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|30328230|gb|CD011492.1|CD011492
EST:     CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTG                         G
genomic: CAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttca ... tcattttcag-
EST: gi|71881928|gb|DT030983.1|DT030983
EST:     TCAGCTGATTATTTGCCAATTGTGG                         TCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTA
genomic: TCAGCTGATTATTTGCCAATTGT-Ggtcattttca ... tcattttcagTCATTTTCAGTATCTCGGTTGTCTCTCCTGTTGAAATCGATTGGAATTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGTTTCAGGTATAATAGACTCATTCGTGTACCATGGTCATAGGGCAATCAAGAAGAAGATGGAACTTGGGAAATTCAGCTGATTATTTGCCAATTGTGgtcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT