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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG

Basic information

species Vitis vinifera
transcript Vv05s0020g01520.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g37390.1 (Oryza sativa), 3'ss of exon 3
aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgctttt--gaa----ttgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
     ||   | || ||   ||  |   | | | |  |    | |   |  |||   |||    |     |  |  ||   || |  ||||  |||    ||||||||||||||||| ||||| |||||| |  ||||||| ||  |||| || ||||||||||| ||||| ||||| ||  |||||||||||||||| ||||| |
-----catttttatgttc-tttcgtagatatcagaagtccttgaatctacaaatcagcattctgattgctcactgctatccatctttttttctgaaacatttgcagCCAGGTTATGAGCGTCTTTGCTGCCTCCGATGCATACAGACACGAGACCACAACTTTGCAACCACTTGTGTCTGTAGGGTCCCCAAGCACCTCAGGGAAG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
-------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
       | |  ||   ||    |    || ||  ||| || | |     | ||  || ||   || ||     |   |||||  ||   ||       ||||||||| ||| ||||| |||||||||||| || | || || ||  |||| || ||||||||||| ||||| ||||| ||| |||| || |||||||||||||| |
aaatctcacatgcacattggacctcatatatttagtcttaatgttgtggtccaatttgcatggccaactgactgagtttttttgcattggat-------aattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG----
      |   | | ||||| |  |||||  |||    | ||||      ||   ||    ||| |||      ||| ||  ||  |  | ||  |||      |||||||| ||||| || || |||||  |  ||||||| ||  |||| || ||||||||||| || |||||||| ||||||||||||||||| || || ||||    
ttttagatgcaaatgctga-agatgctt--ttttgtcacaagagtttgtcaggcatt--cttatatcaaatgtatcattgcttctttttgtgtgtttt-----cagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 4
----------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
          |   | | ||||| |  |||||  |||    | ||||      ||   ||    ||| |||      ||| ||  ||  |  | ||  |||      |||||||| ||||| || || |||||  |  ||||||| ||  |||| || ||||||||||| || |||||||| ||||||||||||||||| || || ||||
cactttttagatgcaaatgctga-agatgctt--ttttgtcacaagagtttgtcaggcatt--cttatatcaaatgtatcattgcttctttttgtgtgtttt-----cagCCAGGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 3
--------aaaaacagg-ctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
        | |  ||   |    |  |||||  |||    | ||||      ||   ||    ||| |||      ||| ||  ||  |  | ||  |||      ||||| |||||||| || || |||||  |  ||||||| ||  |||| || ||||||||||| || ||||| || ||||||||||||||||| || || ||||
cactttttagatgcaaatccagaagatgctt--ttttgtcacaagagtttgtcaggcatt--cttatatcaaatgtatcattgcttctttttgtgtgtttt-----cagCCGGGTTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGCGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
aaaaacaggctgatatttgcttaatttctctaaaagataaaa---gcaaagatgaatttacatctccaaaatcct---tttttaatgatatgctt--ttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
      | | |    |||| ||    ||| ||    || ||    |      || | |  ||  ||    |||||   || ||| || ||   ||       |||||||||||||| || || || |||||| |  | ||||| ||  |||| || ||||||||||| || || ||||| ||||||||||||||||| || |||||||
------atgttttgctttgttt--cctctataggttatgaagtttgtggttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatcct---tttttaatgatatgcttt--tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
       |  |  | | | |   || |  || ||   |          |     |      ||    |||||   || ||| || ||   |||      |||||||||||||| || || || |||||| |  | ||||| ||  |||| ||||||||||| || || ||||| || ||||| ||||||||||| || |||||||
-----ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgcttaatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 5
aaaaacaggctgatatttgcttaa--tttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
    |  |  | |   |  || |   ||| | | |    |  |  |   | |   ||    | |    |||    |  | ||| | |   | |||||||||||| |||||||||||||| |||||| |||| |||||||| ||||| |||||||| ||||||||||| ||||| ||| | || |||||||| || |||||||
--gtattgttttactgtcactaagattttatttgatttgtgcattctgtgttttcttggattttgagtaattaaatcatcatgtttttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGCAACTTAGGGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 4
-----aaaaacaggctgatatttgcttaatttctctaaaagata-aaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
     |    ||    ||| |||  || |||| |  |    ||    ||      || ||||  |   |  ||||| ||     ||| | |   | |||||||||||| |||||||||||||| |||||| |||| |||||||| ||||| |||||||| ||||||||||| ||||| ||| | || |||||||| || |||||||
gttttactttcaccaagat-tttatttcatttgtgcattctatgtgtagttttcttggattttgagtacttaaatcatt-----atgtttttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTACCCAAGCAACTTAGGGAGG

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 3
------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
       | ||| |  | | || |   ||  || | || |  | |   ||     || ||||   |    |||      ||||  |  |     |||||||||||||| |||||||||||||| ||||||||| | || ||||| |||||  ||||||| ||||||||||| ||||| ||| | || |||||| |||| |||||||
atctctgagaactg-ttaaaatata--tagcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttgg---tttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG

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|110388722|gb|EC953500.1|EC953500
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110408210|gb|EC973836.1|EC973836
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|77588197|gb|DV223308.1|DV223308
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110390257|gb|EC955158.1|EC955158
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|71873094|gb|DT022149.1|DT022149
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110703965|gb|EE081360.1|EE081360
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|161712823|gb|FC062346.1|FC062346
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110411061|gb|EC976761.1|EC976761
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110384284|gb|EC948712.1|EC948712
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|71868362|gb|DT017417.1|DT017417
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110694079|gb|EE070869.1|EE070869
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110390488|gb|EC955400.1|EC955400
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110684956|gb|EE062823.1|EE062823
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|34319429|gb|CF372183.1|CF372183
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|71873619|gb|DT022674.1|DT022674
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|77577432|gb|DV217443.1|DV217443
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|110412093|gb|EC977828.1|EC977828
EST:     GCATGGATCAAGGCTATGCAGACCGCAATCTAATCGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
EST: gi|30297281|gb|CB974075.1|CB974075
EST:     GCATGGATCAAGGCTATGCAGATCGCAATCTAATTGCAAAGTGGAAGAAG                         CCGGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC
genomic: GCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttca ... tgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
                            ttttaat  putative branch site (score: 3)
                                       tgctttt  putative PPT
                   aaaatccttttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG

aaaaaca
- - - - - - - - - - - - - - - -aaaagat
- - - - - - - - - - - - - - - - - - - -aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatatgc