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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagtctatatctctcatattagtacatgcagtcataata...

Basic information

species Vitis vinifera
transcript Vv18s0001g13410.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G058910_T01 (Zea mays), 5'ss of exon 11
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattc--ttgc----tggttaactataagcttgatatg---tttcgtg--gaaattatagagtctatatctctcatattagtacatgcagtcataata
|||| | |||||||| |||||||||||||||||||||||||| ||||| |||||||||||  | ||| | ||  ||  ||| |||||| |  ||   |||||  || ||||| |  |   ||||    || || |||      | ||| ||   ||  |||    |||| || |  || |   | |    || |  | |  ||        
TTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGCTTGTTACTTGCAACACTCTATCTTATAATCCGGGAGAAGAAACTAGCTTCACAGgtt-tgcccactagtcttggttgcattttgcttcacttatcattggatctgtagttctgtgctacaattctaaaacctgt---tttggagttggatcgtttagc-------

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G104418_T01 (Zea mays), 5'ss of exon 2
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagt-ctatatc----tctcatattagtacatgcagtcataata-----------------------------------------------------------------------------------------------
||| || ||||| || ||||||||||||||||||||||| || ||||| |||||||||||  | ||| | ||  |   ||| |||||| |  ||   |||||  ||||| || |  ||||| | |     |      || || ||| |    | | | ||| | | ||| | |    | |   ||| | |||  | ||  |                                                                                                   
TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtt-tgtcctctag--tcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA06G03040.1 (Glycine max), 5'ss of exon 11
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagtctatatctctcatatt-agtacatgcagtcataata-
 |||||||||||||| ||||||||||| ||||| ||||| |||||||||||||| ||  | || ||||| ||  |||  || || |||||| | ||||||||| |   |||  |||  | |    ||     | |   ||| ||||| | |   | || ||  | |  | ||  |  | || | |      | | |    | 
ATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGCTTATTACTGGCGGCTTTGTATTTAATAATCAGAGAGAAAAAATTTGCAAGTCAGgtacttaacacatgatcatggggtatttgtattgaatctga-atgttcccttttatttttat-gccagtgtcagttttgtttaatgttgttaataacggcag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA04G03010.1 (Glycine max), 5'ss of exon 11
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagtctatatctctcatattagtacatgcagtcataata
 ||||||||||| |||||||||||||| ||||| ||||| |||||||||||||| ||  | || ||||| ||  |||  || |  |||||| ||||||||||| |   | |  |||  | |    ||     | |   ||| ||||| | |      ||||   | | ||                              
ATTCCTTTTTGCCGTAATGTTTGGTGACTGGGGGCATGGCATATGCTTATTACTGGCGGCTTTGTATTTAATGATCAGAGAGAGAAAATTTGCTAGTCAGgtacttaactcatgatcatggggtatttgtattgaatctga-atgttccctt----ctatattatttttaag----------------------------

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 11
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaat-tatagagtctatatctctcatat-tagtacatgcagtcataata-
 |||||||| ||||| ||||||||||||||||| |||||||||||| |  | ||||||||  | || || ||  | || ||||||||| || | || ||||||||         | |  ||    |||    |    || | | |     | ||||| | |    ||   |   ||    | || |  |     |  |  || 
CTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGCATTCTGCTTGCAACTATGTACTTGATATTGAAAGAAAAGAAACTTGCCAGCCAGgtaataatactccaactgatgtcacttacgagtg---ttaacacgcgagattgaaatctgtctcatcagcagaacttgcttataatttagctgtttgttttac

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 5'ss of exon 11
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtcca-------------ctggattcttgctggtta-actataagcttgatatgtttcgtggaaattatagagtctatatctctcatattagtacat-gcagtcataata---------------------------------------------------------------------------------
 ||||| |||||||| ||||||||||| ||||| |||||||| ||| |  | ||||||||  | ||||| ||  | |  ||||||||| |||| || ||||||||  ||              ||   |||   |||   | | |||||| ||| | | | |    ||||   | | ||  | || ||  ||   || | ||     | | | |                                                                                  
CTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGCCTGCTGCTTGCAACTATGTATTTAATATTGAGAGAAAAGAAACTTTCCAGCCAGgtaatacccctaattgacagcatctattttccgactgagcacagtataagattggtttctgtttcagaaaaagttgtgtgcaaatttcaaattcaagaaaattattttgagagttgttactttgattggtcatcaatgtttgtctttcttgcaagttctagatgctaaaccatcaatccttgcttcgtgacaacag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S60_200V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgta-atgtccact------ggattcttgc------tggttaactataagcttgat-atgtt-------tcgtggaaattatagagtc--tatatctctcatattagtacatgcagtc-ataata---------
 ||||| ||||| |||||||||||||||||||| ||||| || ||  ||||| | | | |  | ||| || |  | || ||||||||  |    |  |||||| || |    |       || | || |      | | |   ||||    || | |||||       |    ||||||  ||| ||  || | ||  |||  ||  |  |  | |  || |||         
CTTCCTGTTTGCGGTAATGTTTGGTGATTGGGGTCATGGTATTTGTCTATTATTGGGAGCGCTTTATCTCGTGCTGAATGAAAAGAATCTCGGAAAGCAGgtatatttttgttttgtggagacttttacagccagtagatgcttatatttctgttcatgttcaaactataagtgaaatttaagattccttaaaacttacatgctaaaaattaaattttatgatactgttgcag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagtctatatctct---catattagtacatgcagtcataata------------------------------------------------------------
 ||||| || ||||| ||||||||||| |||||||||||||| |||||| | || |   |  | ||| || |  | || || |||||| ||   ||  ||||||| | |  |  | |        ||  |  |   |    ||   | | |||  ||   ||| | | | | | |   || || |    |  |   | |                                                                
ATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGCTTACTTCTGGGGGCACTTTATCTCGTATTGAATGAGAAGAAACTTGGAAGCAAGgtaattttc--taaagtggaatatattcccc-tgcacacagtagaatccttggtgatctaagaatttttctttttgttcacatcatcttaacccccctttgcttcaagatttaggtgacatttgagatctgtgataacctaaaattcagaattgtaactgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagtctatatctctcatattagtacatgcagtcataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggaaa