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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

Basic information

species Vitis vinifera
transcript Vv00s0186g00020.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
atggatgactctcctcctgttttcttttcaactcctagcattcccattc--ccccaccccacaagtgaatt--tttgtaaaatttttat---tttgtggttg-------catagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
              | || | ||     |||||  |    |  | ||        |    |   | |||||  |||  ||| |||| ||   ||||||||||         ||||||||||| ||||| ||||||||||| ||||||||||| ||| |   ||| ||||||  ||| || |||||||| || || || || || ||||| ||||
--------------tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
atggatgactctcctcctgttttcttttca-actcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
    ||      ||  |||  ||  | ||| | |   |   |     ||     |           ||||||       ||| |  ||     ||   |||||||| || ||||| ||||||||||| ||||||||||| ||| |   ||| || |||   || || |||||||| || || || || || ||||| ||||
-actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G26840.1 (Arabidopsis thaliana), 3'ss of exon 1
atggatgactctcctcctgttttcttttcaactcctagcattcccatt--cccccaccccacaagtgaatttt----tgtaaaatttttattttgtggttgc---atagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
          ||| | | | || ||    ||       |||     ||           || | | |   | |    | ||   ||  |  | | || |||    ||||||||| |||||||| |||||||||||||| |||||||| ||| |   |||||| |||  |||||| ||||| || || || |||||  | ||||||||||
---------actctttcaggttactaccaaaagagagccatgtgatttagttattgtttcatatgcggtctctaacgtttattgttccttctatatgtttgttttatagGATGGAAACGAGGTTTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAGAAGCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTG

upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaa-aatttttatt--ttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
   | ||   ||      ||| |   | ||  |  | | |||   |    |  |    | |      ||   |||| |||  ||  |  || |  |||  ||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||| ||||| || ||||| ||||| || ||||| ||||
---gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
                  |||||   |         | | |    | | | |  |   |      |||  |||  || ||||          |||  ||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||| ||||| || ||||| ||||| || ||||| ||||
------------------gtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttc---------ttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ27988 (Selaginella moellendorffii), 3'ss of exon 1
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
                             | | ||     |  | | ||| |  |||  |  |  |  || |||    || ||   |          |||||||| ||||||||||||||||||||||| |  | |||||||||  ||||||| ||| | || |||||  |  | ||||| |||||     |  | ||||
---------------------------gtagccccctctgt--cgaatcctcttccctccgtgctatcttatgtgcggttgtttcctc---------tagGATGGGAACGAGGTGTTCTTTAGGATCAAGAAGAACACCCAGTTCAGGAAGCTGATGACCGCCTATTGCCAAAGGCAGTCGGTGGAAGCTGATGCGATTG

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|83274614|gb|DV938711.1|DV938711
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|30131236|gb|CB916575.1|CB916575
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110362534|gb|EC926077.1|EC926077
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110406696|gb|EC972278.1|EC972278
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|77580965|gb|DV219411.1|DV219411
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|71887989|gb|DT037044.1|DT037044
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110696149|gb|EE074982.1|EE074982
EST:     AAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|28965138|gb|CB344171.1|CB344171
EST:     ATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: ATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110427154|gb|EC993585.1|EC993585
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|28959551|gb|CB339776.1|CB339776
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|32250199|gb|CD716018.1|CD716018
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|28958754|gb|CB339370.1|CB339370
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|71888318|gb|DT037373.1|DT037373
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110689180|gb|EE065180.1|EE065180
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|37186608|gb|CF605961.1|CF605961
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110407135|gb|EC972730.1|EC972730
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110373930|gb|EC938937.1|EC938937
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110383948|gb|EC948354.1|EC948354
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|34545171|gb|CF513403.1|CF513403
EST:     GAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: GAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110728228|gb|EE103615.1|EE103615
EST:     AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTANGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCATGGACCAAGGAGCTCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG
             acaagtgaatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
-tggatga
- - - - ctctcct
- - - - - - - -cctgttt
- - - - - - - - - - - - - - caactcc