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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcatt-ttcaatgattttcag--------
|| |||||||| || || || |||||||| |||||||||||||| || ||||| || || |||||||| ||||| | | |||   |    | ||   | | ||||    | |   | |     ||  |  ||   ||   |||  | |||    | ||      ||  | |||  ||| |          
GTAGGAGCACAGACAGAAACTGAGCTTAAGGAAAAGAAACTGAGGGTTGAAGATGCACTGAATGCAACCAAGgtgaatacttctctttgttaatataatttaattttgggattgcattcagagagccttctgatgcacatagagta-tatgggtttgttgtttgttacttaatagtttgctctgtggcag

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaa---tttctttcatgaaattatggcactgaattgctagttg-ctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||| |||||||||||||||||||| || ||||||||| ||||||| ||||||||||| ||||| || |||||     ||||||||   || || |   | |   | |     || ||   |   || |||      ||   |||                                       
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag---------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgta---atttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||| |||||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || ||||||    ||||||||   || || |     |  ||| ||  |   |  | ||   |   | |   | ||   |   | | | |                             
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttt-----tagatttcttttgaattctgtttctgtaagcta--atagtttgttgactttcag----------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagt-tgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
|||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || ||||| ||||  || ||  |  |     |  |  ||    || |  |  || ||| |  | ||   |     |  ||   ||| |||   |                      
GTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAGgtgattttctttatccagctg----atggggttataggtatcgtgctactcatgtat-atcttaattatatgacctcattgagtttcag---------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||||||||||||||||||||||||||| || |||||| | ||||| ||||| ||||| ||||| || |||||||  || |   | |    |  ||  |||| || |   | |    ||     || ||       |   || |  | |||| |||                        
GTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAGgtaacatcatctctaagcaaagagccttgaaatgtt---tccatccatatggtagagactaagttgttggacc--ttttaattag------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttct--ttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||||||||||||||||||||| || ||||| |||||  ||||||| ||||| ||||| |||||||| ||||| ||||    ||  |||   |   | |  |   || || ||||  ||| ||  ||   ||  |  | |  ||     |||    ||                        
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcg---tgttatttgc--atactcgtgaactataactaatcaggattttaattcttcag------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||| ||||||||||||||||| || |||||||||||  | ||||| ||||| ||| | |||||||||||||||| |   |    ||   |     | ||   ||  |||   |||  | ||                                                          
GTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGgtaaatagatcg--gattctggaatattgtggtgtaagtgtttaaattgcag---------------------------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ33580 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
||||| |||||||||||||||||  | |||||||||||  | ||||| ||||| ||| | ||||| |||||||||| |   ||   ||   |     | ||   ||  |||   |||  | ||                                                          
GTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAGgtaaatagattg--gattctggaatattgtggtgtaagtgtttaaattgcag---------------------------------------------------------

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|33401980|gb|CF207607.1|CF207607
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAAAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|26259554|gb|CA810617.1|CA810617
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCGATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|110363904|gb|EC927535.1|EC927535
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|351022937|gb|FQ428846.1|FQ428846
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|351030401|gb|FQ432339.1|FQ432339
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|110419196|gb|EC985406.1|EC985406
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|37188314|gb|CF607663.1|CF607663
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|351036299|gb|FQ458674.1|FQ458674
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCCGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCCCTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|110688028|gb|EE066108.1|EE066108
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|349807747|gb|FQ402138.1|FQ402138
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|351034062|gb|FQ447979.1|FQ447979
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAAGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|110362655|gb|EC926202.1|EC926202
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|110362851|gb|EC926408.1|EC926408
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|34549838|gb|CF518070.1|CF518070
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|33401795|gb|CF207422.1|CF207422
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA
EST: gi|351022922|gb|FQ428831.1|FQ428831
EST:     AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG                         GCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCCGAGA
genomic: AGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctt ... tgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag

- - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - -  AAGAAA