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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG

Basic information

species Vitis vinifera
transcript Vv13s0047g01210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                         ||  | |     ||  | ||      |   || | |||     | || ||  ||| |    |||   |  | | || |||||    | ||  || | |||         ||||||| ||||||||||||||||| |||||||||||||| ||  |||| |||||||| ||||| || || || ||||| ||||||||||||||||| |||||
------------------------gtattattccctcctggttctgctattatggcatataatattctgtgagaaccaattta---tgtacatgtgatatatgctaa----ttaatcttttgttg-------ttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                            |     |   || | || ||| || |   |  |||||                |||| |  | | |  ||||   || |  ||  |||    ||        || |||||||| |||||||| || ||||| |||||||||||||| || ||||| |||||||| ||||| ||  | |||||||| |||||||||||            
----------------------------gtacagtttttttttctcgccaaatattcaggaatta--------------cttgatttactatat--tttt---ctcaatctgaaaagagGTACC------TTTCCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA------------

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                             | |  |  ||  |||||  |  |         |||  |            |||    | ||| |  |||  |  || |    |||| || || |    ||     |||| || ||||||||||||||||| |||||||||||||| || ||||| |||||||||||||| || || |||||||| ||||||||||||||| | |||||
---------------------------gtattattccctcctgcttctcttattatggtgtattttattc---------tctatgatcttgatatgttcaaatctgatatatgaatttcct-taccttggcgttcagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagac-caaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                                      |||| |   |  || |   |  | |   ||||      | ||  | || | |  |||   || | |    |     | ||    |        ||  ||||||| |||||||| || ||||| ||||||||||| || || || || |||||||| ||||||||  | |||||||| ||||| ||||||||||| |||||
-------------------------------------attattccaacttaaaatgtaggacaaaggaagtagctcagaacttcatatatgttttatcttcacga-gtcaaaaaatatgaaaacatacacgttttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
----gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggc-taacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
     ||||| || || | ||   | |||        | |  ||  | | ||   |||  ||| | | |||||           ||| |||| | | || | | |||  |||    ||  | | |  ||  | |   |  |||||||||||||||| |||||||| |||||||||||||| ||| |||| |||||||| ||||| ||||| |||||||| |||||||| ||||||||||||||
gtaattgagttttgttataccttgtcattccccttcaaaagttt--gatagcaataga--aaatattgagaagtttttgg----ctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttt-taggctaacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
      |||  |||   |      ||  |  |        |   ||    |  |    ||||| |    | |        ||| |||| | | || | | | |  |||    ||  | | |  ||  | |   |  |||||||||||||||| |||||||| |||||||||||||| ||| |||| |||||||| |||||||| || |||||||| |||||||| ||||||||||||||
---gtaattgatctgttagacc--ttgtggttccccttcaaaagtttgatagcattggaaaat-attgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
-----------------------------gtgagtattattcttccaatttat----ttaagactgataacttatgcttgcccaagaccaaaaaattagaag----ggaaaaaaaatctgatc--tgttgtttggttttaggctaacgcttg-------aaatttctattg-gatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                              |    |||   |||| ||   ||     ||| |  |   |   | |    |  ||||   |||||  | | |    || | ||||  | |||   | ||| ||||| |     |   | |||        ||| | ||||  | |  |    |||||||||||| || |||||||| ||||||||| |||| ||| |||| |||||||| || ||||| || |||||||| ||||| |||||||||||||||||
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttt-taggctaacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG--
|| | |  | || |   |     | | |  |   |  |  | | |||      |   ||||  | ||   |         ||| |||| | | || | | | |  |||    ||  | | |  ||  | |   |  |||||||||||||||| |||||||| ||||||| |||||| ||||||||  ||||||| ||||| || |  |||||||| |||||||| ||||||||||||||  
gtaattgattttttgttagaccttgtcattcccctt-caaaagtttgatagcaatagaaaatattgagtagtttttgg--ctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G24580.1 (Glycine max), 3'ss of exon 5
-----------------------------gtgagtattattcttccaatttat----ttaagactgataacttatgcttgcccaagaccaaaaaattagaag----ggaaaaaaaatctgatc--tgttgtttggttttaggctaacgcttg-------aaatttctattggatgat-tcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                              |    ||  | |||| ||   ||     ||| |  |   |   | |    |  ||||   |||||  | | |    || | ||||  | |||   | ||| ||||| | |   |   | ||         ||| | ||||     || |   |||||||||||| || |||||||| ||||||||| |||| ||| |||| |||||||| || ||||| || |||||||| ||||| |||||||||||||| ||
gtatgaaatcttctatttacttgtttaatattgtcatcttccttcaaaagaatgaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtgatttttgtgtttatataaaataatctttattatgctatattttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATTGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtattattcttccaatttatttaagactgataac-ttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatct-gttgtttggttttaggctaacg-cttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                             | |||   |  | | ||| || || |  |        ||        |||  | || |  ||| |||||||||    |  |  |||   || |   |||  |  ||  ||||||| |||||||| || ||||| |||||||||||||| ||  | || || || || ||||| || || |||||||| |||||||| ||||| ||||||||
---------------------------gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaa--cagacccagttctttggttttttattttcatcttctcatatgctttgtgtt-ttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG

upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                     |   |   |||  ||| ||     |   ||| ||   |   |                ||| |  |||   ||   |  |   ||   | ||  |      |||  |  |   |||| || || || || ||||||||||||||||||||||| ||| |||| ||||| || || || || || ||||| || ||||| || ||||||||||||||
---------------------ttcgtgttactagtaagttgaagctcttcaaaacttcaggttc---------------tcttacatgtgtctttagtgcactttattacatgtcacaaggcttgc-tattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
                   ggctaac  putative branch site (score: 2)
                                                ttccc  putative PPT
                            ttgaaatttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG