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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccg--tggtattgttttc--atgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
|||||| ||||  |||||||| ||||| || | |||||| ||||| || |||||||||||||| || || || || || || |||||||| ||||||||||| ||  | || || ||    || |   ||  |  || || | ||  |  ||  || |||| |  || |  ||   |||  || | || ||                       
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagt-caaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttt--tgtcactgtatttttag---------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 4
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatg-atggcctgttggctaccgtg-gtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 ||||| |||   ||  |||| |||||  |||||||||||||||| ||| |||||||||| ||  ||||| |||| ||  |||||||||| ||||| ||||| || | |    |  ||||  |      ||   || || |  |||  |    | | |       |  ||   ||   | || ||  || |                     
ATTTGGTGGAGTATTGCTGGCTATGTGTACAAATGATTTTATTTGCTTCCATGACTGGGCAGAGGGCAGGATGATACGCAGAATTGATGTCAATGTGAAAgtgagtaattttgttcatggattcaaatttattttgcgtgtcatttgga----atattatgatgctaaataggatccgctttcttatttgtag-------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 ||||| |||   ||  |||| |||||  |||||||||||||||| ||| |||||||||| ||  ||||| |||| ||  |||||||||| ||||| ||||| || | |    |    |  | |    |    |     |||  |  ||  | | |       |  ||   || | | || ||  || |                     
ATTTGGTGGAGTATTGCTGGCTATGTGTACAAATGATTTTATTTGCTTCCATGACTGGGCAGAGGGCAGGATGATACGCAGAATTGATGTCAATGTGAAAgtgagtaattttgttcctggatttaaatttttttttgcgtgtcatt-tggaatattatgatgctaaataggatctgctttcttatttgtag-------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 14
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaaca--tgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 | ||| |||   ||  | || || ||  |||||||||| |||||||| ||||||||||| || |||||| |||| || |||||||| || ||||| ||||| ||   | ||   || |       ||| ||||       |||||| |  |     |||   ||           ||  ||  |  | | | |  | |             
ATATGGGGGAGTATTGCTTGCTATATGTACAAATGATTTCATTTGTTTTTATGACTGGGCAGAGTGCAGGTTGATACGTCGAATTGACGTGAATGTAAAAgtgagtcgttacttttgcttcagcaatggatacccatcatgtgtttttactcttttttgccttaacgccactggaattgattactcttgtgcctggtgtag-----------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 2
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 ||||| || ||| ||||||||||||||||||||||||| || || || ||||| ||||||||||||||| ||||||| || |||||||||||||| ||||||||  ||  ||||| |     |  |||  |       || ||| ||  |    | |              |||| ||| ||  |||| ||    |||   | | ||||
ATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGGCTGAATGCAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagtgcttgcatgaggtgacatcagctttc-------tgcttttatttcttcttac--------------tgtttcttgttaattttgttaaaattttcttgtgtcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 ||||| || ||| ||||||||||||||||||||||||| || || || || || |||| ||| || ||| ||||||| || |||||||||||||| ||||||||  ||  ||||| |     |  |||  | || | || |||           | |     ||  |||||| || ||| | ||                         
ATTTGGCGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTACGATTGGGTTGAGTGTAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagtgcttgcatgaggtggcatcagctttc-tgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcag-----------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatg-gcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 || || || |||||| |||| |||||||| || ||||| || || || ||||||||||||||||||||| ||||    || |||||||| ||||| |||||||| |||   || | | | |   | | || | || | || |  |  |    |  ||    | || |||   ||||  || | |  | ||                    
ATTCGGTGGCACTTTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagtactttgattaggtgacatctagttatc-tgctcttttccttcttattcgttgtttaatttaattt--tgttatttatcttgtgtcag------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatg-gcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag
 ||||| || ||| || |||| |||||||| || ||||| || || || ||||||||||||||||||||| ||||    || |||||||| ||||| |||||||| |||   || | | | |  || | || | || | || |  |  |    || ||    |  | |||   ||||  |  | |  | ||                    
ATTTGGTGGCACTCTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagtactttgattaggtgacatttagttatc-tgctcttttccttcttattcattgtttaatataattt--tgttattaatcttgtgtcag------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 17
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgat-------ggcctgttgg---ctaccgtggtattgttttcatgccacactg-caggaattgattaaatgttccttttttcttttctttttttttcactatttcag-----------------------------------------------------------------
|||||| || || |||||| |||||||||||| ||||||||| || |||||||| ||||| ||||| ||| ||||| | ||||| ||||||| ||||||||||||  || | ||          |  |  || |   ||||      || ||||  | |  ||  |  ||| |||   || | ||      |         ||  || |     |||| |                                                                  
TTTTGGTGGGACGTTATTGACAATGTGCTCAAGTGATTTTATATGCTTCTATGATTGGGCGGAATGTAGGTTGATTAGGCGAATAGATGTTACTGTCAAAgtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaac---------atgatggcctgttggctaccgtggtattgttttcatgcca-cactgca----ggaattgattaaatgt--tccttttttcttttctttttttttcactatttcag--------------
|||||||||||| || || |||||||| || |||||||| || || |||||||| ||||| |||||||||||||||| || ||||||||| |  || || |||  || | ||          |  ||    ||| ||   | |    || ||   || |   |  | ||        |   || || ||  |||   ||  | |  ||  |   ||  || | |                
TTTTGGAGGAACCTTGTTAGCAATGTGTTCGAATGATTTCATCTGCTTCTATGATTGGGCCGAATGCAGGCTGATTCAACAAATTGATGTCACCGTAAAGgtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacact-------gcaggaattgattaaatgttcctt---------ttttcttttctttttttttcactatttcag------------------------
 ||||||||||| || || || ||||| |||| |||||| || || || ||||| ||||||||||| |||||||||| ||| ||||| || | ||| || |||  | |    |   ||||    |   |     |   ||   |||| | || | |       |  | || | ||   ||   | |          ||||| |   || ||| ||| ||| ||                           
CTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGGCTGAATGTAGGCTGATTCAACGTATTGACGTCACTGTAAAGgtatcc-cagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcag

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|351030017|gb|FQ430759.1|FQ430759
EST:     ATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAA                         AACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACA
genomic: ATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcacta ... actatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT