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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtcactttgtacgtgctgcaattttcaggtctttaaaggaggatagcccaaatttactaatttgtcatcaaatttttgtttccacttctag

Basic information

species Vitis vinifera
transcript Vv09s0018g01780.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G02580.1 (Glycine max), 5'ss of exon 8
TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgta---ata-gtcactttgtacgtgctgcaatttt-----------caggtctttaaaggaggatagcccaaatttactaatttgtcatcaaatttttg-----tttccacttctag--------------------------------------
 |||||||| || || ||||| |||||||||||||| ||||| |||||||  || |||||||||||||| | ||||||||||||||| |||||||||||||||   |||  ||| | |  |     |||||||||           |  |||||| |    | ||     || || | ||||    | | |||           | | |  | ||                                        
GTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCAGGAGAATTTGACACTGAGgtatgtatatatcattatccaaaaaatgcaattttttttttctggcctagtctttcagaatgaatgttttaatttaattaatggaccctaaaaaacaaaaggaatatgccatactgatcaaaaagatttgtcgttgacttgaaccttgaacctag

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA08G23440.1 (Glycine max), 5'ss of exon 8
TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgta-----ata-gtcactttgtacgtgctgcaatttt------------caggtctttaaaggaggatagcccaaatttactaatttgtcatcaaatttttg-----tttccacttctag-------------------------------
 |||||||| || || ||||| |||||||||||||| ||||| |||||||  || |||||||||||||| | ||||||||| ||||| |||||||||||||||     |||  ||| | |  |     ||||| |||            |  |||||| |    | ||     || || | ||||    | | |||           | | |  | ||                                 
GTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTTGATCTTGTAAAGATTATTACTGACATTAACATTGCTGTTGAATCCGGAGAATTTGACACTGAGgtatatgtatatatcattatccaaaaaatgcaaatttattttttctgacctagtctttcagaatgaatgttttaatttaattaatggaccctaaaaaacaaaaggaatatgccatactgatcaaaaagctttgtcgtggacttgaacatag

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA15G00560.1 (Glycine max), 5'ss of exon 8
TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaat---agtcactttgtacgtgctgcaattttcaggtctttaaaggaggatagcccaaatttactaatttgtcatcaaatttttgtttccacttctag---------------------------------------------------------------
 |||||||| || || ||||| |||||||||||||||||||| |||||||  || || ||||||||||| |  |||||||| ||||| |||||||||||||||||   | | | |   || ||  |  || | |      ||||    |      ||| |||  |  ||| | | || |  |   | | |  |     |                                                                
GTATGTGGAGACAGCTGATCGGCCTGGATTACTGGTGGATCTTGTAAAGACTATTACGGACATTAACATTGCCGTTGAATCCGGAGAATTTGACACTGAGgtaattaaattaaataaatatgtagtcaaaatgtacaacttttattcaaa-----cccgaatgcatcaatatat-ataatgtaactatatttagagagaatgagaaaaggggtgtctcagtcacagtcacggtcacatctgaaaggtttgctgtaaaacgtag

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G44740.1 (Glycine max), 5'ss of exon 8
TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtcact--ttgtacgtgctg-caattttcaggtctttaaaggagg-----atagcccaaatttactaatttgtcatcaaatttttgtttccacttctag
 |||||||| || || ||||| ||||||||||| |||||||| |||||||  || || ||||||||||| |  |||||||| ||||| |||||||||||||||||| | |    |  ||  | | | |||  | ||    | ||| | |       | |      || |   | |      | |||  ||||||   |    |||
GTATGTGGAGACAGCTGATCGGCCTGGATTACTTGTGGATCTTGTAAAGATTATTACAGACATTAACATTGCGGTTGAATCCGGAGAATTTGACACTGAGgtaataattatatatcatatatacagtcaaaatgcatcaatataatgtaattatttagaaaagggatgtctcagtcacatctgaaaggtttgttgtaaaacgtag

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|29784297|gb|CB344831.2|CB344831
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110375956|gb|EC940987.1|EC940987
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110386695|gb|EC951311.1|EC951311
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110411796|gb|EC977519.1|EC977519
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|111125066|gb|EE253677.1|EE253677
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|349823504|gb|FQ414914.1|FQ414914
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGGTTGTTGGCCAAGGCAAAGTTTCAT
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCAT
EST: gi|110372559|gb|EC936737.1|EC936737
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110387079|gb|EC951719.1|EC951719
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|29784413|gb|CB345109.2|CB345109
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110385943|gb|EC950505.1|EC950505
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110413183|gb|EC978960.1|EC978960
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|110372429|gb|EC936593.1|EC936593
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC
EST: gi|29785638|gb|CB342854.2|CB342854
EST:     GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAG                         GGTTTGTTGGCCAAGGCAAAGTTTCGTGTCAGCTACCGCGGAAAAGCCATC
genomic: GCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtca ... ccacttctagGGTTTGTTGGCCAAGGCAAAGTTTCATGTCAGCTACCGCGGAAAAGCCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGTGGAAACTGCAGATCGCCCTGGATTACTGGTGGATCTCGTAAAGAGCATCACTGACATTAACATAGATGTTGAATCAGGAGAGTTTGACACTGAGgtaatagtcactttgtacgtgctgcaattttcaggtctttaaaggaggatagcccaaatttactaatttgtcatcaaatttttgtttccacttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA