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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa...

Basic information

species Vitis vinifera
transcript Vv14s0108g01030.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatg-tgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttag---aagaaaagtggatccg-ttgatcgaaaaaa
||||||||| ||| ||||| | || || ||||||||||||||||| || || |||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |  |||       | |  || |  ||| | | |       | |   ||  | |  |  ||     | ||| |||| ||     | ||  |     
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta-----

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os03g25980.1 (Oryza sativa), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataa---atgtg-attttgattaatat-tcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa--------------------------------------------------
  ||||||| || |||||  | || || || ||||| || ||||||||||| |||||||| || || ||||| |||||||||||||||||||||||||||||||||    |||| |||||  ||| | | | ||| | |  |||   |    ||  | ||| |    || || |   ||||   |  |||   |  || |  | |                                                  
TTCAGTTGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGTGGCTACTGTAAGCTCCACCTGTCATATTCTCGTCATACTGATCTCAATGTAAAGgtataataggtgtgcattttctttagtgtattatgggcatgaaacctgtttagacgatatg-atttactgccatcatagaacccttcatcttgtattcaagcacagactttcctatcatatgaattatgaaccatgtatctgtctgttctttcag

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G082174_T03 (Zea mays), 5'ss of exon 10
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaat-gtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
||| ||||| ||| ||||| | |||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||  |||||     | |  || || ||| |||   ||   | |   | | | | ||     | ||  ||    | ||  ||  |  ||||| 
AGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatagtagttttgggctgtgtaaattagcaaataatttaagtatatactgt-tcaggactaatgaataacgaattctgctcaattagtaaaaaaag

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G082174_T05 (Zea mays), 5'ss of exon 7
-------------AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaat-gtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
             ||| ||||| ||| ||||| | |||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||  |||||     | |  || || ||| |||   ||   | |                                                 
ATATAACTACCGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTgtaagcttcatctgtcatactctcgtcatactgatctcaatgtaaaggtataaatagtagttttgggctgtgtaaattagcaaataatttaagtatatac------------------------------------------------

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G178169_T01 (Zea mays), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaat-gtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
||| ||||| ||| ||||| | |||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||  |||    |  | |  || || ||| |||   ||   | |   | | ||| ||     | ||  ||    | ||  ||  |  |||| |
AGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaattgtagtttcaggttgtgtaaattagcaaataatttaagtatatatcgt-tcaagactgataaataatgaattctgctcacttagtaaaaaaga

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM5G883601_T02 (Zea mays), 5'ss of exon 9
-------------AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataa-atgtg-attttgattaatattcat-gagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
              || || || || |||||  | || || || ||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||||| ||||| ||||||||| | ||| |||||| ||| ||||| | |   | ||||        ||                                                   
ATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTgtaagcttcacctgtcatactcccgtcatactgatctgaatgtgaaggtataataggtgcattttgtttagtattctttgctcataaaacccttctagat--------------------------------------------------

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM5G883601_T01 (Zea mays), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataa-atgtg-attttgattaatattcat-gagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa-----------------------------------------------------
 || || || || |||||  | || || || ||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||||| ||||| ||||||||| | ||| |||||| ||| ||||| | |   | ||||        ||  | |  || |  | |  | | || |      | |    |    ||| |                                                       
CGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGATCTGAATGTGAAGgtataataggtgcattttgtttagtattctttgctcataaaacccttctagatgatacatatacccctt-tcacaaaaccctcagttatagtacaggaacaggacaccctgtattgttttttttgacatacgaagttatgccccttcatatttcag

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA18G49580.1 (Glycine max), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaa----tgtgattttga-ttaatattcatgagaa-aaaaataagaggggaaaaaatgt-aaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
  ||| ||| | ||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    |||| || ||| ||||| ||| ||||   |||||| | |  ||    ||| | ||||   |||||||||| || |||||  | ||||||       
-TCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGGtataaaaatatgtgtttatgagttaatgttcttgaggggaaaaatgaaaaaggggggaatattaaagatatccttagaagcaatgtggacac-ttgatcag-----

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA09G37080.1 (Glycine max), 5'ss of exon 10
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaa----tgtgattttga-ttaatattcatgag-aaaaaaataagaggggaaaaaatgt-aaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
| ||| ||| | ||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    |||| || ||| ||||| ||| |||| |||||||| | |   |    ||| | ||||   |||||||||| || |||||  | |||||||      
ATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaaaatatgtgtttatgagttaatgttcttgaggaaaaaaatgaaaaatgggggaatattaaagatatccttagaagcaatgtggacac-ttgatcg------

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA11G21330.1 (Glycine max), 5'ss of exon 9
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgtgattttgattaat-attcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtgga---tccgttgatcgaaaaaa--
| ||| ||||||| ||||||||  ||| || ||||||||||||||||||| ||||||||||| |||||||||||||| |||||||||| | || |||||||||||||| | || ||||| |   | | ||  || ||||    |||||| |      || | |  | |||| | | || ||| |   |   ||||||  ||| |  
AACAGCTGCCAAAAAAGCTCTAATGGGGCATTGCATATATGATGGTGGCTGTTGTAAGCTTCGTCTATCATACTCTCATCATACTGATATTAACGTAAAGgtataaat-tcatcttgatgagggaataatatgagaaaagggggagggggat-----tagaattatacttatatgcaatgtgaaaattttcttgatcagaaatatt

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 5'ss of exon 7
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaa--------tgtgattttgattaatattcatgagaaaaaaa-------taagaggggaaaaaatgtaa-agtcttccttagaagaaaagtggatccgttgatcgaaaaaa------------------------------------------------------
|||| | ||||||||||| || || ||||||||||| ||||| |||||||| ||||||||||  |||||||||||||||||||||||||| ||||| |||||| | |        ||   ||||||    | | | | | |||||||       | || ||   | ||  ||||  |  || | ||             ||      ||| |  ||                                                      
AGCAATGGCCAAAGAAGCACTGGAAGGACACTGCATTTATGACGGTGGCTACTGTAAGCTTCGACTATCATACTCTCGTCATACTGATCTGAATGTTAAGgtacataagatttgttgcttttttgagatgtgtacctaaaaaaaaaaacaattgtgaggggaagagaatagtaacggaattgcgtatgcttctttcttttctacatttcgcagcaaaatattaaatcaacgtctaattatcttcttcaattttcctgtgattgaatgaag

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 5'ss of exon 9
------AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa
      ||  |  || |||||||| || || || |||||||| || ||||| || |  || ||||||||||||||||||||||| ||||||||| | |||||||||||||   | |  || |  |   | ||  ||  |    |   |    |     | | |   | |  | |   ||   || | |   |  ||| | ||  | 
TACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGATTTAAATgtaaaggtat---tctccttcttgtaggt-ttgttgctagcccatgcatgatgacttcactatgtggacagcatctaaaattaaatcg--tctctgacctaatcat

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110418311|gb|EC984453.1|EC984453
EST:     ATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAG                         GCACATAGTGATAGAAGTAGAGATTATACAATCCCAGATTCAGGTCTGCTT
genomic: ATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgt ... gtctttgtagGCACATAGTGATAGAAGTAGAGATTATACAATCCCAGATTCAGGTCTGCTT
EST: gi|110412027|gb|EC977759.1|EC977759
EST:     ATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAG                         GCACATAGTGATAGAAGTAGAGATTATACAATCCCAGATTCAGGTCTGCTT
genomic: ATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgt ... gtctttgtagGCACATAGTGATAGAAGTAGAGATTATACAATCCCAGATTCAGGTCTGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgtgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttagaagaaaagtggatccgttgatcgaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgaaaaa