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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatactttgcagcttgatcag...

Basic information

species Vitis vinifera
transcript Vv15s0024g01470.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0024g01470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G07390.1 (Glycine max), 5'ss of exon 7
GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatac-----tttgcagcttgatcag---
||||||| ||||||||||||||   ||| |||| |||||||||||  || | || ||||||||||| || |||||||| |||||||| |||||||| |   | |||| | ||||       |||  |||| | | || | || |     | |   |     |     | ||  |      ||||   ||   |      
GCCAGATGTTTCTGAGCTGGAGTTGAAGTTTTCTGAACAATCAAAAATATTGTTGAATCTTCAACAAAAAGTTGATGACTTGGCATCCAAGgtttactgcaa-ttctcaaccca-------cttctctttgatagttatatgatatgactgtagctggaaatagatcagaagcatgaatttttgtttctctttttcttt

upper sequence: Vv15s0024g01470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G07310.1 (Glycine max), 5'ss of exon 7
GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatactttgcagcttgatcag-----------
||||||| ||||||||||||||   ||| |||| |||||||||||  || | || ||||||||||| || |||||||| |||||||| |||||||| |   | |||| | ||||       |||  |||| | | || | || |     | |   |    |  | | |  |  |  ||| |  ||  |              
GCCAGATGTTTCTGAGCTGGAGTTGAAGTTTTCTGAACAATCAAAAATATTGTTGAATCTTCAACAAAAAGTTGATGACTTGGCATCCAAGgtttactgcaa-ttctcaaccca-------cttctctttgatagttatatgatatgactgtagctg---gaaatagatcagaagcttgaatttttgtttctctttttcttt

upper sequence: Vv15s0024g01470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G29280.1 (Glycine max), 5'ss of exon 7
GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatactttgcagcttgatcag-----
||||||| ||||||||||||||   ||  |||| |||||||||||  || | || ||||||||||| || |||||||| |||||||| |||||||| |   |||||| | ||||   ||  |||  |||| | | || | || |    |   | |     |  |   |  |  |  ||| |  || ||        
GCCAGATGTTTCTGAGCTGGAGTTGAAATTTTCCGAACAATCAAAAATATTGTTGAATCTTCAACAAAAAGTTGATGACTTGGCATCCAAGgtttactg-aacttctcaacccac--tt--cttctctttgatagttatatgatatgatatctgtagctggaaattaatcagaagcttgaatttttatttctcttg

upper sequence: Vv15s0024g01470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G17620.1 (Arabidopsis thaliana), 5'ss of exon 6
GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatactttgcagcttgatcag--------
 |||||| |||| || ||||||||||| |||||||||||  | ||| | ||||  |||||||||||||| || ||||| |||||| ||||||| |  | |   |||    ||||||      |    ||| ||  ||  ||   | ||| |||    |||||| ||| || |     |  |  |   ||||        
ACCAGATGTTTCAGAACTGGAGACAAAACTTTCAGAACAGGCCAAGATTCTCTCTAATCTTCAACAGAAAGTCGATGACTTGGCAGCAAAGgtgtgcttttgtttc----cccataaagagttatgttttgactcttaactacagaactcatt---tactgtttcat-cagacttaatatatttcactcagcttattac

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|26259606|gb|CA810669.1|CA810669
EST:     AGAAGG-TGATGATTTGGCATCAAAG                         CATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
genomic: AGAAGGTTGATGATTTGGCATCAAAGgtttattctg ... tgcattttagCATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
EST: gi|110700983|gb|EE078116.1|EE078116
EST:     TGATTTGGCATCAAAG                         CATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
genomic: TGATTTGGCATCAAAGgtttattctg ... tgcattttagCATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
EST: gi|110383268|gb|EC947629.1|EC947629
EST:     CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAG                         CATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
genomic: CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctg ... tgcattttagCATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
EST: gi|110373786|gb|EC938134.1|EC938134
EST:     CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAG                         CATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
genomic: CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctg ... tgcattttagCATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
EST: gi|110375221|gb|EC940185.1|EC940185
EST:     CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAG                         CATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG
genomic: CAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctg ... tgcattttagCATGCATACAACCCAGATGAGGAGTATGAAGAAGTGGAATCCCAGTTGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGATATTTCTGAGCTGGAGACAAAGCTTTCAGAACAATCAAAGTTACTCTTAAATCTTCAACAGAAGGTTGATGATTTGGCATCAAAGgtttattctgacttcttagcccatagttgacttgcctttcacaattgtctgttggacttattattcactgttacatacaaatactttgcagcttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atacaaa