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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctactcattttaactttctagttcaaagttcaaacaattttacataccaatattcagaaaagaagaggacttttagcagtaaatcaatcacattattcacatatctgattggtttggttcttcattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG

Basic information

species Vitis vinifera
transcript Vv09s0002g02430.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA08G20780.1 (Glycine max), 3'ss of exon 10
gtgagcctactcattttaactttctagttcaaagttcaaacaattttacataccaatattcagaaaagaagaggact--tttagcagtaaatcaatcacattattcacatatctgattggtttggttcttcattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG
                                |  ||||     | ||||    || |  ||   || ||   || |  |||  |  ||  || ||  || ||  || |  | |  | || ||     |   ||||  ||||| |||| || |||||||| ||||||||||| || |||||||||||  |  | ||| | ||||
------------------------------gtaaatcaactggctctacaattgaaaaaacatgtaataaattgaattgtttttctctatttctatt-cactaagcaaaggttttgtgggctt-----tcatttttacagGCTTTAGAGAAATGTCAGCTTAAGGCAACAATTAGTAGTCTTCCAAATCTCTTGGACACTTCTG

upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgagcctactcattttaactttctagttcaaagttcaaacaattttacataccaatattcagaaaagaagaggacttttagcagtaaatcaatcacattattcacatatctgattggtttggttcttcattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG
                                                  |   ||||   |  |||||    || ||  |          ||||| |  ||  | | ||||   || |       ||| ||||| |||||||||| ||||||||||||||| |||| || |||| |||||| ||    || || || || |
-------------------------------------------------gtga-aataacaaacaaagactgagatttcca----------aatcaaaagatataaa-atctttctgataaaaccattctttttgcagGCTCTAGAGAAGTGTCAGCTCAAGACAACGATTAGCAATCTTCCTAATAAACTTGATTCTTCAG
















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|110695449|gb|EE073482.1|EE073482
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|110715223|gb|EE093024.1|EE093024
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|22011601|gb|BQ796635.1|BQ796635
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|30303963|gb|CB980757.1|CB980757
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGAAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|30300210|gb|CB977004.1|CB977004
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|30303898|gb|CB980692.1|CB980692
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|110359216|gb|EC920349.1|EC920349
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|219555058|gb|FG984847.1|FG984847
EST:     GAACTAACTTGGACCCTCTAGGCTTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|22011602|gb|BQ796636.1|BQ796636
EST:     TTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: TTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
EST: gi|29785172|gb|CB341926.2|CB341926
EST:     AACTAACTTGGACCCTCTAGAGC-TTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGG
genomic: AACTAACTTGGACCCTCTAG-GCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGG
EST: gi|219555135|gb|FG984396.1|FG984396
EST:     GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAG                         GCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG
genomic: GAACTAACTTGGACCCTCTAGGCCTTTACTCTGACAATGAAATATGGGAGgtgagcctac ... cattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaatcaatcacattattcacatatctgattggtttggttcttcattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG
                         atctgat  putative branch site (score: 4)
                                        ttcttcatttt  putative PPT
            acattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctactcattttaactttctagttcaaagttcaaacaattttacataccaatattcagaaaagaagaggacttttagcagtaaatcaatcacattattcacatatctgattggtttggttcttcattttgaagGCTCTAGAAAAGTGTCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA