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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTGACCGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatccgttcagtgacaaatattgcgttgacaattgtttctattcaagccctctgaaatgtgattaatctatgttcttcaaatgttgcacttcctgttttccattcataatgagaagctagaaattaataaccaagtgtttggcag

Basic information

species Vitis vinifera
transcript Vv04s0023g01040.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA02G06720.1 (Glycine max), 5'ss of exon 10
ATTGCTGACCGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtac--ttatccgttcagtgacaaatattgcgttgacaattgtttctattcaagccctctgaaatgtgattaatctatgttcttcaaatgt-tgcacttcctgttttccattcataatgagaagctagaaattaataaccaagtgtttggcag
 ||  |||| ||  | |||||||||||||| |||||||| |||||||| | ||| ||||||||  | | |  | | ||||  ||||     | || | ||  |  | ||||     || |  || | |      || |||   ||||| | ||   ||   |                                                  
GTTATTGACTGGATCAATCCTGGCTCACGAAATGATGCACGCATGGCTTAGACTTAAAGgtactatcagctttcctgtgatcaataccatttagaaacttagtatt-ttca---tttcagtgatttaacagtgttaagttggacaaatttgtgggattatggcag-----------------------------------------------

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 11
ATTGCTGACCGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatccgttcagtgacaaat-attgcgttga-caattgtttctattcaagccctctgaaatgtg--attaatctatgttcttcaaatgttgcacttcctgttttccattcataatgagaagctagaaattaataaccaagtgtttggcag
 ||| | |||||| | ||||| ||||| ||||||||||||||||||||   ||| || |||| |     |  || |  |   | |||  ||||| ||||||    ||   ||        ||||||    ||  ||| |||   ||    |                                                              
TTTGTTAACCGGGTCAATCCTTGCTCATGAGATGATGCATGCATGGCTTCGACTAAATGgtaatctgaagaacactcccttctcattatgttgagcaattgaacgtagggaaatatcaaaaaatgttttgttgctctgtgtatatctgtag--------------------------------------------------------------
















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|110368327|gb|EC932299.1|EC932299
EST:     CGGGACGATCCTGGCTCATGAGATGATGCATGCATGGCTCAAACTGAAAG                         GCTATCGAAATCTGAGTCAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
genomic: CGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatcc ... tgtttggcagGCTATCGAAATCTGAGACAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
EST: gi|110715090|gb|EE092739.1|EE092739
EST:     CGGGACGATCCTGGCTCATGAGATGATGCATGCATGGCTCAAACTGAAAG                         GCTATCGAAATCTGAGTCAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
genomic: CGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatcc ... tgtttggcagGCTATCGAAATCTGAGACAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
EST: gi|110397911|gb|EC963898.1|EC963898
EST:     CGGGACGATCCTGGCTCATGAGATGATGCATGCATGGCTCAAACTGAAAG                         GCTATCGAAATCTGAGTCAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
genomic: CGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatcc ... tgtttggcagGCTATCGAAATCTGAGACAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
EST: gi|30137737|gb|CB923075.1|CB923075
EST:     CGGGACGATCCTGGCTCATGAGATGATGCATGCATGGCTCAAACTGAAAG                         GCTATCGAAATCTGAGTCAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
genomic: CGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatcc ... tgtttggcagGCTATCGAAATCTGAGACAGGATGTTGAAGAAGGCATCTGCCAGGTGTTGG
EST: gi|110731744|gb|EE106423.1|EE106423
EST:     CGGGACGATCCTGGCTCATGAGATGATGCATGCATGGCTCAAACTGAAAG                         GCTATCGAAATCTGAGTCAGGATGTTGAAGAAG-CATCTGCCANGTGTTG
genomic: CGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatcc ... tgtttggcagGCTATCGAAATCTGAGACAGGATGTTGAAGAAGGCATCTGCCAGGTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTGACCGGGACGATCCTGGCTCACGAGATGATGCATGCATGGCTCAAACTGAAAGgtacttatccgttcagtgacaaatattgcgttgacaattgtttctattcaagccctctgaaatgtgattaatctatgttcttcaaatgttgcacttcctgttttccattcataatgagaagctagaaattaataaccaagtgtttggcag

- - - - - - - - - - - - - - GAGATG