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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag

Basic information

species Vitis vinifera
transcript Vv17s0000g06640.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 4
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
  ||| | | | ||| ||||  | || |  || ||||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||| |||||    ||||        |  |  |  |||  | ||     |  | |     |  |    |||| | | |                                                                                         
AGTGCGGCTTTGGCACTGGACCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACAAAAGAAGAAATGGAACTTCTCAAGgtaatacaatgtttggccttgttgtgatctcatctgaaaactatgttggcttactgtct-cgtttttttccag--------------------------------------------------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os04g17130.1 (Oryza sativa), 5'ss of exon 9
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
  ||| | ||||||  ||||||| ||| || |||| | ||||||| |||||||||||||||| || ||||| || |||||||||||||||||||| |||||      | ||   |||     |||| |||  |    |  |    | || |||        |||||| || |||  || ||     |||| | |  | | |   |||| || ||                                            
AGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgttgttttaaaattaaagcttatatttccttgcactccttctgtaatctttaat------ttttctcttctctgaatatcttgcaaaagtaaagta-tttgcactttttcctatcag------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G414002_T02 (Zea mays), 5'ss of exon 7
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
  ||||| |||  |  | ||| | || |  || ||||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||| ||||||||     ||||| ||  || |||   ||    |  |  | | ||  |   |  ||    || ||| || |     | ||| ||||                                                                       
AGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAGgtgca----caacacgag--attattgctttactggcatggtcacctcatgttttaaaa---ttttcttct-tactccttttttttgacag--------------------------------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G398731_T01 (Zea mays), 5'ss of exon 3
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
  ||| | ||||||  |||| || ||| |||| |||| ||| ||  | |||||||| ||||| || ||||| || |||||||||||||||||||| |||||       | |   ||    ||||||||  | |||||| |     | ||   |   |     ||  |      |  ||   | |||   || ||  || | | |                                                      
AGTGCTGCTCTAGCTTTGGACGATTCAGTTTTGGATGCTGACCAGATTGAAAATCTAATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAGgt-tgtttttgaattaatatctaattttccac-atgtttgaaccatttttttctctgaa----tccata----aaaaataaattttgcacattttt-tccatcag------------------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G11100.1 (Glycine max), 5'ss of exon 10
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcag--caataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgt--ttatttag
|||||||| |||||  ||||||||||| | || |||||||||||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | |||||| ||   || ||    |  |||||||  |||  || ||   ||| | ||| |         | | |||  | || ||    || |  |  |      | || |  |||    |  || ||||     || |   |  |   |  ||||| |  || |||||
GCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAGgtgaagtttaacaaatttatccataatt--cttacatcttgttttaacaattaa---------ggtttctagtttgtggtatcttctgtaacactaaaatatatccttttactgtgatttgtttaatttctaattttgtttcctcttgtttatggttgtttag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA05G00820.1 (Glycine max), 5'ss of exon 8
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcag--caataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgt--ttatttag
|||||||| |||||  ||||||||||  | || |||||||||||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | |||||| ||   || ||    |  ||||   |||||  || ||   ||| | |||      |||   ||||    ||||      | ||||      |    | || |  |||    |  || ||||   | || |   | ||   |  ||||| |  || |||||
GCTGCAGTACTAGCTTTGGATGAGTCGGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAGgtgaagtttaacaaatttatccata--cttcttacatcttgttttaacaatt------aaggt-ttctagtttgtggcatcttctgttagactaa--aatatatccttttactctgatttgtttaatctctaattttgattcctcttgtttatgattgtttag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA06G21190.1 (Glycine max), 5'ss of exon 10
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataatt--ttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgttttt----ctttcttagtttttccccttagactaatgatttctgtttgtttatttag
|||||||| || || |||||||| ||| | |||||||||||||| |||||||||||||| || || || ||||| |||||||| || || ||| | |||||| |||  ||||| || | |||  |  |||||  || || | ||  | |||       |   ||||||   | |     |   |||| | |||     ||||||| || ||     ||||||  ||||     || || ||||  |   | |  |||||| |||
GCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAGgtgaagct-taaca-aatttatacatgattcttgcatcttgctttgacaatt-------aagggttctcatttctagcatttgctgtt-actatgaatttctaccttttattgtaattttcttgcttttctaattttgattaatcttggttatg-gtttatatag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 5'ss of exon 7
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagac-taatgatttctgtttgtttatttag
||||||||||| ||||||||||||||  |  |||||||||||||| | || ||||| |||||||| ||||| || || ||||||||||| || ||||||||   |   | ||    |    | |    || | | ||||  |   || |   | | |||   | | ||   | | |    || |||  |||  |  |  || |||| ||     | |||  ||   ||| | | ||||  | |  |||||||    |||
GCTGCAGTTCTGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAAGTTTTGCCCAACCAAGGAGGAGATGGAGCTACTTAAGgttacgtcttgacttttg----agtagcattatctatttctgtctttact---ttggagatcatttgtgaaat-atgtcaattattggttatcattattcacttgttattgaca-tgagtccttgttcttggtcgtaattgtctg-gtttgttc---tag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G07760.1 (Arabidopsis thaliana), 5'ss of exon 16
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatt-tag
||||||||||||| ||||||||||||  |  |||||||||||||| | || ||||| |||| ||| ||||| || || ||||||||| | |||||||||||             |  || | | |||    |  ||  || || ||| |          |  ||| | || |   |    || |||  |||  |  |  || ||||  |       |||  ||   ||| | |   | |||    || |||| || |||
GCTGCAGTTCTAGGAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAGGTTTTGCCCAACAAAGGAGGAGATGAAGCTTCTTAAGgt------------tacctcttgacttt----tgagtagcactatctactt---------ctgtctttactttt--gtcaattcttggttatcattattcacttgttagttgacacgagtcattattcttggtc--gtaattg--attggtttgttgtag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 5'ss of exon 4
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
 ||||||| || ||||||||||||||  |  |||||||||||||| | || || || |||||||| ||||| || || ||||||||||| |||||||||||   |   |   |  |||   | | ||    |    || |||   | |   ||    | |  |   || | | |  ||  || || | | | |      ||  ||| || ||  ||      ||    | |||| ||   || |              
ACTGCAGTCCTGGCAATGGATGAGTCTGTAGTAGATGTTGATCAAATAGAGAAACTTATAAAGTTTTGCCCAACAAATGAGGAGATGGAGCTTCTTAAGgttttgacttttgagtagttgcattatttactttctatttatttattttgtgatatttgtcagttcttggt-taatcatcattattcactttttattgacacgggttcttgttctttg-----tcgtgattgactgatttgttgtag------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 5'ss of exon 18
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
|||||||| |||| |||||||||||   |  |||||||||||||| | || ||||| |||| ||| ||||| || || ||||||||||| |||||||||||  | |  |  |     | |  |   |  ||||  | | |   | | ||   ||  |   || ||      ||    |  |||    || | |||                                                               
GCTGCAGTACTAGGAATGGATGAGTATGTACTAGATGTTGATCAAATAGAGAATCTTATAAGGTTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAGgt-tacctcttgcctttttgagtagcattatctacttcttaa-ggttgttacttgacacgagtccttattcttggtcgtaattgactggtttgttgtag------------------------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G07770.2 (Arabidopsis thaliana), 5'ss of exon 7
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacac----aagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
||||||||  | ||||||||||||||  |  |||||||||||||| | || ||||| ||| |  | ||||| || || ||||||||||| ||||||||||||   |      ||     |||   ||| |     | ||| |       |||| ||  ||   | ||  |||    |||  |  |||||  | ||  ||       |||| |                                                  
GCTGCAGTCATGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATACAACTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAGgtgttacctcttgacttttgagtagcaatatctacttgtgtctt------tatttaagtgat--catttactgacacgag--ttcttgttcggaat--tgactgctttgttgtag------------------------------------------------

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S246_71V6.1 (Physcomitrella patens), 5'ss of exon 8
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtg----cagcaataacacaagtcata----attttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggat--gtttgttgagtatattggtctacctgtttttctttcttagtttttcccct--tagactaatgatttc--tgtttg--tttatttag
  || ||||||  |  ||||    ||  | || |||   |||||||||||||||||||| ||||||||||| || || |||||||||||  | || |  ||      | || ||   ||||| | |    ||| |  |   |||   | |      | ||  |||   ||   | |  ||||   |   ||  |   || | |     | |||    |||    | ||  ||     |  || | | || | ||   ||   |  | | |||||
AGTGGAGTTCTTTCTTTGGACCCATCTGTATTGGATACAGATCAAGTGGAAAATCTCATTAAGTTCTGCCCAACGAAGGAGGAGATGGATATGCTGAGAgtaagtttatcattacttcaagtgaaaggctattgtgattagtgtagaagttctggattaactgaaagtgtcaacggacgtgaatttttattcatgtggtttctcaaattgccttacattcaccatgagcattgtaattggtaaatttattactttattgccgggatgtttttag

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S13_282V6.1 (Physcomitrella patens), 5'ss of exon 8
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag
  || |||||| ||  ||||     |  | || |||   ||||||||||||||||| || ||||||||||| || || |||||||||||   | || ||       | |||   || | | | |||  || ||||  |  ||   | || ||||   ||    |   | ||   |||| |   | || ||||    | | | |  |  |  |||| | || |      |  || |||| ||||||  ||||  || ||
AGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGA-TATGTTGAG-------Agtaagttaattaacattttaattgtatggct-gttgtgtttttaatgattgat-cacgaaggtgattggatatcaat-gattataa-attttgcatactcattattct-acttgtaattactttacgaatgttttctg--tgttatttcag

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|110700830|gb|EE077830.1|EE077830
EST:     TGGAACTTCTTAAG                         GCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
genomic: TGGAACTTCTTAAGgtgcagcaat ... gtttatttagGCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
EST: gi|110700821|gb|EE077821.1|EE077821
EST:     TGGAACTTCTTAAG                         GCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
genomic: TGGAACTTCTTAAGgtgcagcaat ... gtttatttagGCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
EST: gi|37184855|gb|CF604209.1|CF604209
EST:     AAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG                         GCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
genomic: AAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaat ... gtttatttagGCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
EST: gi|110700879|gb|EE077921.1|EE077921
EST:     TGGAACTTCTTAAG                         GCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
genomic: TGGAACTTCTTAAGgtgcagcaat ... gtttatttagGCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
EST: gi|110700824|gb|EE077817.1|EE077817
EST:     TGGAACTTCTTAAG                         GCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG
genomic: TGGAACTTCTTAAGgtgcagcaat ... gtttatttagGCCTATACTGGTGATAAGGAGGCCCTGGGAAAGTGTGAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAGgtgcagcaataacacaagtcataattttcttctatgtttcattagctattcaatggaagacgttctctgctgtgaggatgtttgttgagtatattggtctacctgtttttctttcttagtttttccccttagactaatgatttctgtttgtttatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA