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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct...

Basic information

species Vitis vinifera
transcript Vv10s0071g00210.t01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 19
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatga--agtgattatcatctgaactcgcattc-agtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct
||| |||||||||||||| |||||||| ||||| ||||| || ||| |||||||||||||||||||||| |||||||||||||| || ||||| || |||||||| | |  ||   || |  | |  | || | | |  |||  | |  |    | ||| | |  ||||          |      |      |||||| |  
AGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAAGTTGGGTACACAAAATTGTTCTTTCGAACTGGCCAGgtgagctaagcagcctttgttttatttattcacttcctggtaatgagtgtattgccaataactgttggccttg---tttttctgaatgagcgttaaatgtttg

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 19
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgatt--atcatctg--aac--tcgcattc---agtagggtgattgaccctaatgagttgtggctggaaaa--caatgtcac-----tttgttaataaatgctct---------------------------------------------------------------------------
||||||||| ||||||||||||||||| |||||||||||||| ||| | ||||||||||||||||||||||||||||| ||||| |||||||| |||||||| || |  | | |||  ||  ||||  ||    | ||||    | ||     |||| |  | || |  |||   | ||  |  || ||||       ||| |  ||| |||                                                                               
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGACAGgttagttctatttattcaattttctgccaatggccacattagaaactaaatctattg-ctttcattacatgtttatagaccattcattgtcttggatttttatctatatatgtatgtactattttatttttgttttaagcatttggtgaaactaatcttgtgttactttgtccttcgatattgggctgaag

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 19
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgatt--atcatctga----actcgcattc---agtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct----------------------------------------------------------------------------------
||||||||| ||||||||||||||||| |||||||||||||| ||| | ||||||||||||||||||||||||||||| ||||| |||||||| || ||||| || |    | |||   |   |||       || ||||    | |   |  |||      | |   |  |    |   |   ||    ||   ||  | |    | |                                                                                  
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGTCAGgttagttctgtttattcagtttcctggcaatggtcacattagaaactgaagctatttgtttcattacatgtttatagaccattcattgttctggattttttaccattatatgtatgcacgaccttttttatttgttaagcatttggtgaaagtgatcttgtgttactgtgtcctttgatattgggctgaag

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct--
 ||||| |||||||||||||||||||| ||||||||||| |||||| |||||||||||||||||||||||||||||||||| ||||||||||| || ||||| |    | |||| | |  | |||| |   || || |    |  ||    |    || |           |  | |  ||  |  ||  ||||        
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatg-aatgtgaatttt-tttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaa---taaatgctct---
 ||||||||||||||||||||||| || |||||||||||||| ||| |||||||||||||||||||||||||||||||| | || |||||||| || |||||     || ||   ||  || |    |  ||   | ||   | |||    |  || | |||| |  | |||  ||||| ||| |  | |   || |   ||    
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgtatatagatgtctataaaattt---tttacacgaattattctcatt---tcatataaattgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA20G00320.1 (Glycine max), 5'ss of exon 20
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattg-accctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct---
 ||||||||||||||||| |||||||| ||||||||||| |||||| || | ||||||||||||||||||||||||||||| |||||||| || || ||||| | |     | ||| |  |   || |   || || |    |  ||  | ||    || |  | | |     ||  ||| ||||| | ||  ||    ||   
GGATCCACTTAGTGTTTCGGTTGCAATTCTTCATCAGTTTAATATTTTGTCGGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGGACAGGGCAGgtaataaatgttaatttt--ttaaaagttttatacaatttttttcttatatcccccagaatctttgattatctacg-tgt-actttttaaactaagaaactttg

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA20G23660.1 (Glycine max), 5'ss of exon 20
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtg-attgaccctaatgagttgtggctggaaa-acaatgtcactttgttaataaatgctct
 ||||||||||||||||||||||| || |||||||| ||||| ||| |||||||||||||||||||||||||||| ||| | || || ||||| || ||||| |   || ||   ||   | |  || |   ||    |      ||| |   |  ||      |  || ||   |||||    | |   |  | |   |  
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAATTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACGAAACTATTCTTTCGAACAGGGCAGgtaaatagatgtctataagttttttacacatttttctcatttcatattaattgttgtggcaaacgaatgtaattgcaatgattttatagaatcagaaatt--

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct
|||||| || |||||||| |||||||| || |||||||| |||||  |||| |||||||| ||||||||||||||||||||||||||| |||| || |||||   || |     |  || |||||  ||          |||  |   |     |    || |  ||| |  | | |    |||    | |  |      
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataac----tagtcgtctgatgtcttgactttaggggccacaaatt---agacattcttactgcagtatact--tgcttcaccattgcag-----

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 5'ss of exon 20
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct
|||||| || |||||||||||||| || || |||||||| |||||  |||| |||||||||||||||||||||||||| ||||||||| |||| || |||||   ||     | || ||  |||     |  |  |  |   | |||     ||| | |  |      ||     ||||  | |||              
AGATCCTCTAAGTGTTTCAGTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgtataata----gcttgtcggctg-----gtgtcaaagacttttatt--ttataaggggcaggaataagagtctcatgt-gcattgcag-----------

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 5'ss of exon 23
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct
                    |||| || || |||||||| |||||  |||| |||||||||||||||||||||||||| ||||||||| |||| || |||||   ||     | || ||  |||     |  |  |  |   | |||     ||| | |  |      ||     ||||  | |||              
--------------------TTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgtataata----gcttgtcggctg-----gtgtcaaagacttttatt--ttataaggggcaggaataagagtctcatgt-gcattgcag-----------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa