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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

Basic information

species Vitis vinifera
transcript Vv00s0186g00080.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
||       |    |   || ||   |  |||  |  |    |   ||    | |   |   |   | ||||  |    |  |  ||     |||||||||||||||| ||||| ||||||||||| ||||||||||| ||| |   ||| ||||||  ||| |||||||||||||| || || || || ||||| ||||
tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaattttttta-aaatgttc-----ttttctggttg-------tgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
              || |  |   |      ||||   |       ||   | ||        | |||||| |||| |||| |||     |||| ||||||       |||||||||| || ||||| ||||||||||| ||||||||||| ||| |   ||| || |||   || |||||||||||||| || || || || ||||| ||||
-------------actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaa--tgttctt--ttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
    | | || ||    | ||| |   | ||  ||     |||   |   | |||    | |      ||    ||| |    ||  |  || |  |||||||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||||||||| |||||||| ||||| || ||||| ||||
----gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
                         ||||     |  |  |   |     |  ||| |  |   |||| |       | || |  ||| |  |||||||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||||||||| |||||||| ||||| || ||||| ||||
------------------------gtttttggtattgagaaaatcgtatataatactcttct--tgaagtaacaatcattggtaatttttc-ttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G26840.1 (Arabidopsis thaliana), 3'ss of exon 1
tatggatagttctgctcttgttttcttttcaacttccaccat----tcccatccttgtaccccacaagtgaatttttttaaaatgttcttttc------tggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
           ||  |   | || ||    ||      ||||    |    |  ||||  |  |   |     |    |  | ||||| ||        | ||| | |||||||| |||||||| |||||||||||||| |||||||| ||| |   |||||| |||  |||||||||||| || || || |||||  | ||||||||||
----------actctttcaggttactaccaaaagagagccatgtgatttagttattgtttcatatgcggtctctaacgtttattgttccttctatatgtttgttttatagGATGGAAACGAGGTTTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAGAAGCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTG

upper sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ27988 (Selaginella moellendorffii), 3'ss of exon 1
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
                              | |  || |  | |  |||||  | || |    |||   | || |     ||| ||| ||       |||||||| ||||||||||||||||||||||| |  | |||||||||  ||||||| ||| | || || ||  |  | ||||| |||||     |  | ||||
----------------------------gtagccccctctgt-cgaatcctcttccctc---cgtgctatcttatgtgcggttgtttcctc------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|22009992|gb|BQ795026.1|BQ795026
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110700427|gb|EE078455.1|EE078455
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|34545460|gb|CF513692.1|CF513692
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|110715752|gb|EE094161.1|EE094161
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|77583211|gb|DV220644.1|DV220644
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|46917740|gb|CN547069.1|CN547069
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|160482170|gb|EY254983.1|EY254983
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|34545546|gb|CF513778.1|CF513778
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|27585742|gb|CB008437.1|CB008437
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|254917816|gb|GR903468.1|GR903468
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAG
EST: gi|27584860|gb|CB007555.1|CB007555
EST:     AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAG                         GATGGTAACGAGGTGTTCT
genomic: AGAAGCCCACGGACCAAGGGGCCCACATAAACTTGAAGGTCAAGGGCCAGgtatgtttct ... ggttgtgtagGATGGTAACGAGGTGTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG
                                    ttcttttctg  CT-rich tract
                aagtgaatttttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- tggatag
- - - - - - -gctcttg
- - - - - - - - - - - - - - - - -ttccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaatg