Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaaagaacttcctgaagccatttaagttgctgcttggttggatgatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT

Basic information

species Vitis vinifera
transcript Vv13s0019g05360.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G33330.1 (Glycine max), 3'ss of exon 7
----------------------------------gtataaaaagaacttcctgaagccatttaagttgctgcttggttggatgatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT
                                    |||     |        ||     |||||    || || |    || || |||| |    |  ||||||||      ||| |||| |    | ||    ||||||||||| || ||||| || ||||||||||| ||| |||| || || |||||| |||||||||| |||| |||| |||||||| |   |||    |  
gtaggaatttgttcactaattttttttgcttgcttcatacccccagtacaacaaaaatcattaagcaaatgatttgac--ataatatctttgaccgtaaatgttttatacgtgtttctgttttcttattac----agGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACTGAGAGGGGGGTGATGGAGTAG

upper sequence: Vv13s0019g05360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G34220.1 (Glycine max), 3'ss of exon 7
----------------------------------gtataaaaagaacttcctgaagccatttaagttgctgcttggttggatgatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT
                                   ||||        |  |  ||  |||| |        ||||     || || | || |    |  |||||||| ||  || | | ||     || | |  |||||||||||| || ||||| || ||||||||||| ||| |||| || || |||||| |||||||||| |||| |||| | |||||| |   |||    |  
gtaggaatttgttcactaaaaaaatttgcttgctttataccccagtataacaaaaatcattaagcaaatgacttgac---ataatatatttgacggtaaatgttttatgtgtttctatttt-----tttatta-cagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACCGAGAGGGGGGTGATGGAGTAG
















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|71866666|gb|DT015721.1|DT015721
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|110696981|gb|EE073568.1|EE073568
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|77581507|gb|DV219700.1|DV219700
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|71865533|gb|DT014588.1|DT014588
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|161713236|gb|FC063668.1|FC063668
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|110727604|gb|EE104555.1|EE104555
EST:     TAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: TAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|87586077|gb|DY474538.1|DY474538
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|110391242|gb|EC956204.1|EC956204
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|32460812|gb|CD801986.1|CD801986
EST:     GATATCTGATAGGGGTGATTTCATGTCCGGGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: GATATCTGATAGGGGTGATTTCATGTCC--GGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
EST: gi|110376153|gb|EC941197.1|EC941197
EST:     AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAG                         GAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT
genomic: AGAATAAAGATATCTGATAGGGGTGATTTCATGTCCGGGACAACTGATAGgtataaaaag ... tcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT
                                          ccttcact  CT-rich tract
                 atgttttaagtaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaaagaacttcctgaagccatttaagttgctgcttggttggatgatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA