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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os02g08018.1 (Oryza sativa), 5'ss of exon 7
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcata-gccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
||||| ||||||||  ||||| ||  |||||| |||||||| ||||||||||| || |||||||| || |||||||| |||||     |  ||| |  |    | |  |   |||    ||| | ||     |  | |||   |    | |   | ||||              
GTCCCGGCTGATGGTGTTTTGGTTAGTGGTCATTCTCTTGCCATTGATGAATCCAGTATGACTGGGGAAAGCAAGATCgtaag----caaccttttcgacccctattgtcctatataggactgacttccccatcatatgtaaaccctgtttcttttattag-------------

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G391042_T02 (Zea mays), 5'ss of exon 10
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaattt-catagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
|||||  | ||||| ||  | ||   ||||||||| ||| | || ||||||||||||||||||||||| || || |||||||| |  |  | || |  |    |  || |  || |   ||       |   ||       |    | | ||   |                  
GTCCCCACAGATGGTATCCTTATCAGTGGTCACTCCCTTTCCATAGATGAATCAAGCATGACTGGAGAAAGTAAAATTgtaagttactcca-ttatgcagccttggaagtaacacacatacatgaacctaacttggccaaatggggactatttgaag-----------------

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G140328_T04 (Zea mays), 5'ss of exon 10
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
|||||||||||||| ||  | ||   ||| ||||||||| | || ||||||||||||||||| ||||| || || ||||||||        ||  |  || |   |  |||   ||  || || |||   |      ||   |  |   |    |  | |    | |||  ||
GTCCCTGCTGATGGTATCCTTATCAATGGCCACTCTCTTTCCATAGATGAATCAAGCATGACGGGAGAAAGTAAAATTgtaag--------ctactccaatatgctgctttggaagtaacacactttacct------gtgaacctaacttggccacatgtgggttatttgaag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 12
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
||||||||||||||| |||||||  ||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||  |||||   | | |    |   |||   |  |  | | | |  | | ||||         | |   |||||||| |    | |||  ||
GTCCCTGCTGATGGAGTTTTGATCACTGGTCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAGATTgtaagtgtttatttctatcttgtgaag-aataataaggttaattactgctctcttttcc-----taagtagataataatttttc--tttttgcag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 9
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
||||||||||||||| |||||||  | ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||  |||||   | | |      |  |   ||  |  | | | |  | | ||||         | |   |||||||| ||   | |||  ||
GTCCCTGCTGATGGAGTTTTGATCACCGGTCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAGATTgtaagtgtttatttctatcttg----tggagaacaaggttaattactgctctcttttcc-----taagtggataataattttcc--tttttgcag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 9
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgttt----aaaaatttaatttcatagccactcatttttt-ttttttttgttttctaattcttaataattatcacatctttttag
|||||||||||||||||| ||||  |||| |||||||||||||||||||||||||| |||||||| |||||||| ||||||||  |||||   | | |      |||||  ||||  |  || ||    |  |   | ||||||||| |                             
GTCCCTGCTGATGGAATTCTGATCACTGGCCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAAATTgtaagtatttatttctatctcctgggaaattggattttttttcccctttcctgctacctattttgttttttgcag-------------------------

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 9
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
||||||||||||||| || ||||  |||| |||||||||||||||||||||||||| |||||||| |||||||| ||||||||  || ||   | | |        || ||   |     |  ||| |||| |  |   | | |  || ||   |                  
GTCCCTGCTGATGGAGTTCTGATCACTGGCCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAAATTgtaagtattcatttctatctcctggg--aaattggaatttttttctttcttttctgctaactatttttttttttgcag-----------------

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 5'ss of exon 11
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcatttttttttt-ttttgttttctaattcttaataattatcacatctttttag
|| |||||||||||| |  |||| ||||| |||||||| ||  |||||||||| |||||||||||||||||||| |||||  | |||| |  |  | | | | |  ||||    |    |||  || || ||  | |   ||||||  | | |||  ||  |    ||| | ||
GTTCCTGCTGATGGAGTACTGATATCTGGCCACTCTCTCGCCCTTGATGAATCTAGCATGACTGGAGAGAGCAAAATTgtgtgtttttgt-ttcctgtcatagtaaaattgttgattttctcgcttcttcttggtataactttctatgtgtcaat--ttccctttccttgtcag

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 11
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag
|| ||||| |||||| ||||  || |||| || || |||||| ||||||| || |||||||||||||||||||| ||||||   |||  |   |   | |  ||||      | |   || ||| |||   |||  ||| |||| |       |  || || ||         
GTACCTGCGGATGGAGTTTTAGTTGCTGGACATTCCCTTGCAGTTGATGAGTCCAGCATGACTGGAGAGAGCAAAATTgtatactttattctcttccttagcatttg---caacaaatac-catctttgcatttcatgtgttctgaaaaa-gctgtttctcgcag--------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATTgtaagattttatacttgtttaaaaatttaatttcatagccactcattttttttttttttgttttctaattcttaataattatcacatctttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA