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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggatgttgatatttgtatagatttctaattcaaaattttaattttttcaatctggaatttgaaaagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01800.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G14040.2 (Glycine max), 3'ss of exon 3
------------gtggatgttgatatttgtatagatttctaattcaaaattttaattttttcaatctggaatttg----aaaagggtatgtggtgggaa----tgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
             |  ||| |   |||      ||||| || ||   | | || | ||| |   | | |  || |    ||    | || |  |  |||    | ||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||
gttggattgtcattctatgctttcattgaatccgatttatattttgtattgtttaatttgttgcttttgttttcgctctaattctgcatattatatgaaaatatatagACATAGATGGACTGGAAGGTATGAAGCTCACCTTTGGGATAATAGCTGTAGAAGGGAAGGGCAATCAAGAAAAGGACGCCAAG

upper sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G06010.1 (Glycine max), 3'ss of exon 2
----------------------------gtggatgttgatatttgtatagatt-tctaattcaaaattttaattttttcaatctggaatttgaaaagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
                             | | | ||  | ||| | |  ||  | |||||     |||| |||||| |  |||  | | || |||   ||||        || ||| ||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||| |||||||
gttggatagacattctatgcttcactgaatcggtttttttttttttttgcatggtttaatttgttgtttttatttttgc--tcta-attatgcaaattatatgaaa---atatatagACATAGATGGACTGGAAGGTATGAAGCTCATCTTTGGGATAATAGCTGTAGAAGGGAAGGCCAATCAAGAAAAGGACGCCAAG

upper sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G41180.1 (Glycine max), 3'ss of exon 6
---------------gtggatgt-tgatatttgtatagatttctaattcaaaattttaattttttcaatctggaatttgaaaagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG--
                ||  ||| |    |||      ||||| |||   | | |  | | || | |||     | |||    |  | | |  |     | ||||||||||||||| || ||||||||||| ||  | |||||||||||||| |  | |||||| ||  | || |||||  | ||||  
gttttgaaactttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttgttaatt---gaattgtggtgattgttttcttatcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAGTG

upper sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G51190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtggatgttgatatttgtatagatttctaattcaaaattttaat---tttttcaatctggaatttgaaaagggtatgtggtggga-atgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
|||  |   ||| | |  ||   ||       ||| | |  |||   | | | ||| ||  | ||   ||   | || ||||  | || ||| ||||||||||| || || ||||||||||| |||||||||||||| |||||||| |||||||||||||| |||||  | ||||
gtgtttaa-gatgtctcaattttttcgcgtgacaataataaaatgcgtatataaatttgttactt---aattttttggggtgttatatatagACATAGATGGACCGGTAGATATGAAGCTCATCTTTGGGATAATAGCTGTAGAAGAGAAGGACAATCAAGGAAAGGAAGACAAG

upper sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G20840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtggatgtt-gatatttg---tatagatttctaattcaaaattttaat--tttttcaatctggaatttgaa---aagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
      ||| ||||| ||    ||   | | | | |  |   ||||||  ||||   ||||  | |||||    || | |     |||   || ||| ||| ||||||| ||  | ||||| ||||| || |||||||||||||||||||||||||| || || || |||||  | ||||
------gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatcttta-tttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattttaattttttcaatctggaatttgaaaagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
    ttttaat  putative branch site (score: 3)
     tttaattttttcaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggatgttgatatttgtatagatttctaattcaaaattttaattttttcaatctggaatttgaaaagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA