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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaagaaaaccataaaataaaacaagtatgggccttttttttttcctctttctttttctgcctgctcattcactcacggctttgctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG

Basic information

species Vitis vinifera
transcript Vv15s0021g00640.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------------gcaaaagaaaaccataaaataaaacaagtatg--ggccttttttttttcctctttctttttctgcctgctcattcactcacggctttgctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG
                                                                                           | |        | ||| | |     |   |||   |  ||    | |     || || |||     | |  |   ||   |  |||   | ||  |   ||| ||||| |||||||||||||||||||| ||||| ||||| || ||||| |||||||| ||||||||||| ||||||||||| |||||||||
gtaattagtaacgaagagaagaatgttggaaagattttagggagactcaaattatgaactattggcaaaaacaattcataggcatagtgaagtatgttctcgctatatagttctggagacatgctagtgttacaatctgaaatttactgttttgttttaccaaccaaccgccatcttctttgtgtgtctgcagACAAGTCTCTATAGAGGAAGGAGAAGCAAAAGCACGTGAGCTCAATGTCATGTTTATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------gcaaaagaaaaccataa----aataaaacaagtatgggcctttttttttt---------------cctctttct----ttttctgcctgctcatt--cactcacggctttgctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG
                                                                ||||||  ||  ||||     | || |  | ||    ||  | |  || |                  |  |||    ||| |||  |  |  ||  ||  ||     ||  | ||  |   ||| ||||| |||||||||||||| ||||| ||||| ||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||||
gtaattagtaatgaagagaagaatgttggaatgaatttagggagactcaaattaggaacgactggcaaaaacaattcataggcatagtatagtatgttcttgctatatcattctggagacatgctagtgttacaatctgaaatttactgttttgtttttaccaaccatcttctttgtgtgtgtctgcagACAAGTCTCTATAGAGGAAGGGGAAGCAAAAGCACGTGAGCTCAATGTCATGTTCATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaaaagaaaaccataaaataaaacaagtatgggccttttttttttcctctttctttttctgcctgctcattcactcacggctttg---ctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG
  | | |    |  || | | || || |  | | |  ||  |  | |||  | | |||  | | |||  |||    |   |  ||     | |  |||  |||||||||||| |||||||||| ||||||||| || || || || ||||| ||||| |||||||| |||||||| || || ||||| || |||
-tacagggtttctttatagtcaa-cacgctttgacacttgatggtgcctactacatttgttac-tgccaattgggcctttgtattaaatattttgtttctcagGCAAGTGTCAATAGAGGAAGCAGAAGCTAAGGCACGCGAACTTAATGTAATGTTCATCGAAACCAGTGCCAAAGCGGGCTTCAACATTAAG

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|22015132|gb|BQ800166.1|BQ800166
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|349831044|gb|FQ420714.1|FQ420714
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|351023599|gb|FQ432982.1|FQ432982
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|351034756|gb|FQ458113.1|FQ458113
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|349828935|gb|FQ419268.1|FQ419268
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|110700609|gb|EE077413.1|EE077413
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|349824858|gb|FQ414716.1|FQ414716
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|110424892|gb|EC991267.1|EC991267
EST:     GTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATCGAGGAAGGAGAAGCCAAAGCTCGTGATCTAAATGTTAT
genomic: GTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
EST: gi|110696285|gb|EE075270.1|EE075270
EST:     GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAG                         GCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT
genomic: GATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgtgatgactt ... gctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctttctttttctgcctgctcattcactcacggctttgctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG
                           cactcac  putative branch site (score: 2)
     tttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaagaaaaccataaaataaaacaagtatgggccttttttttttcctctttctttttctgcctgctcattcactcacggctttgctatgctttgacagGCAAGTGTCTATAGAGGAAGGAGAAGCTAAAGCTCGTGATCTAAATGTTATGTTTATCGAAACTAGTGCCAAGGCTGGGTTCAATATAAAG

- - aagaaaa
- - - - - - - -aaaataa
- - - - - - - - - - - aacaagta