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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaagttcatctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 13
----caaaagttcatctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
      |||| |      | | |  ||| |        |   | ||| || || | || | |||| |    | ||||  ||         |  |||   | ||||| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||
gtagtcaaagatggcactgaaataagta-taagatatgagaatgataaatttaattttgaactcttctgatccatctattt--------gttcttttgctgtagATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 12
----caaaagttcatctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
      || | |      | | |  |||  | |   || |  | ||| || |||| || | |||| |    | ||||  || ||||||| ||||||      |||| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||
gtagtcaatgatggcactgaaataagtatatgatatgaca-atgataaatttagttttgaactcttctgatccatctt-tttgtgttta-tgtttt------agATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 17
----caaaagttcatctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
      |||| |      | | |  |||  | |   || |  | ||| || |||| || | |||| |    | ||||        |||  |||||   || ||||| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||
gtagtcaaagatggcactgaaataagtatatgatatgaga-atgataaatttagttttgaactcttctgatccatct--------ttttgtgtttatgttgtagATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 11
------------------caaaagttcat-ctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
                  || |  |   | |||  || |  ||  |  |   | |||  ||  |  |  | ||  |   | |       ||||||   |  ||  | |||| || | |||| |||||| |||||||||| ||||||||||    ||| ||||| || ||||| ||  |||||||||| ||||| |||||||||||||||| 
gtattgtagtcagagtctcacagatgggtactgctatgtaatatgtatgataatatgatatgaaaatgatattcttaatttcgaagtcttctgatgtttccttgcttttttgct-acagATCATTTTTCTGGAAACAATATGCAATGATGTAGACATAATTGAGAGGAATATTCGCTTTAAAATTCAGCAAAGTCCTGACTATGCAGAAGT

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 11
caaaagttcatctggcattttgtagttcagcggaaatgtcat------atatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
      || ||   ||  || ||| |   ||     |  | |      |||||   | |  |  | |||  ||||| ||||||    ||| || | ||   |  |||| |||||| |||||||| | ||||||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||||||| |||||||
-ttgctttgatgcagcgctt-gtaatgttgcatggctaccttcgactaatatcggatttggaattatcc--tcctaactgatttaccttttatctctta--tgcagATCATTTTTCTGGAAACACTATGCAATGATGAGCGCATTATTGAAAGAAACATACGTCTAAAAATCCAGCAAAGTCCTGACTATTCAGAAGA

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|30322291|gb|CD005553.1|CD005553
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|30321972|gb|CD005234.1|CD005234
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|27580319|gb|CB003014.1|CB003014
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|27580309|gb|CB003004.1|CB003004
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|32250239|gb|CD716058.1|CD716058
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|30321898|gb|CD005160.1|CD005160
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
EST: gi|30321402|gb|CD004664.1|CD004664
EST:     CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG                         ATTANNNNNNNGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT
genomic: CAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgat ... ttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA
                                         tgttttcctt  CT-rich tract
                                    tttaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaagttcatctggcattttgtagttcagcggaaatgtcatatatctagtcttaatctctccattcctatctgattcgtgtttaatgttttccttatagATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -ggcattt
- - - - - - - - - - - - - - agcggaaa