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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcgaatagttaaaattgaaagtcgaagaagacatttttaagcctcgttagttttatagttaaaatttcactctcggaatccttttttgtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAGCTTGAATCCTTATGCAGGTCTCTTCAGGCAGAAAGGCGACAAAATTCAA

Basic information

species Vitis vinifera
transcript Vv13s0019g03960.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G31830.1 (Glycine max), 3'ss of exon 12
ttttcgaatagttaaa--attgaaagtcgaagaagac--atttttaagcctcgttagttttatagttaaaa-----tttcactctcggaatccttttttgtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAGCTTGAATCCTTATGCAGGTCTCTTCAGGCAGAAAGGCGACAAAATTCAA
         || | |   |||  |  ||||  | |    |||| | |  |   | | |||| |  || | |     | | |        ||   ||| |||||||||||||||||||| |||||||||||||||||||||  || |||||||||||||| || ||||| |||||| |||| |||||||||||||||   ||||||||  
---------agctgatgcattagacatcgatcatgctcaatttgttactcatatcaattttcttattgacaacatatgtgaaatatattatttatttatgtctgagcagCGGGAGCGCATGAAGAAACAACTGGAGAAAACTAAAAATCAGAAAGAAAAACTGGAATCATTATGCCGGTCACTTCAGGCAGAAAGGAAGCAAAATTCTT
















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|71871908|gb|DT020963.1|DT020963
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATTGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|30326467|gb|CD009729.1|CD009729
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|110726208|gb|EE101788.1|EE101788
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATTGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|110428293|gb|EC994760.1|EC994760
EST:     CTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: CTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|77586923|gb|DV222608.1|DV222608
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATTGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|110693582|gb|EE069938.1|EE069938
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
EST: gi|110727231|gb|EE103758.1|EE103758
EST:     AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAG                         CGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG
genomic: AGAGCAAATCTGAGAAGTCAGATGTCACTCTAATAGAACTTGTTGAGGAGgtaagattta ... gtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgttagttttatagttaaaatttcactctcggaatccttttttgtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAGCTTGAATCCTTATGCAGGTCTCTTCAGGCAGAAAGGCGACAAAATTCAA
                                    tccttttttgtct  CT-rich tract
     tagttttatagttaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcgaatagttaaaattgaaagtcgaagaagacatttttaagcctcgttagttttatagttaaaatttcactctcggaatccttttttgtctgagcagCGGGAGCGCTTGAAGAAACAACTGGAGAAAATGAAGAATCAGAAAGAAAAGCTTGAATCCTTATGCAGGTCTCTTCAGGCAGAAAGGCGACAAAATTCAA

- - - - - - - aaattga
- - - - - - - - - - - - - -aagaaga
- - - - - - - - - - - - - - - - - - - -ttaagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactctc