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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggttttacttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 11
ttgggttttac---ttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG
||  | |   |   |  | |||||| ||| ||  |   | || | ||   |||   ||  |   | |||  ||     | ||| || | ||    |  |||||||||| ||  | ||||| ||| |||||||| |||| |||||| | ||||| ||||| ||||||||||| |||||||| ||| |||
ttaagctgatcaggtggttttttgcatatttaattacacatgacgattactttgctttactgtatgtatttgatatgaacatggtattaca---cttgtgcagAAGAAGCAAAATACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G35560.2 (Glycine max), 3'ss of exon 11
ttgggt---tttacttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG---------------
||  |    |    |  | |||||| ||| ||  |   | || | ||   |||   ||  |   | |||  ||     | ||| || | ||    |  |||||||||| ||  | ||||| ||| |||||||| |||| |||||| | ||||| ||||| ||||||||||| |||||||| ||| |||               
ttaagctgatcaggtggttttttgcatatttaattacacatgacgattactttgctttactgtatgtatttgatatgaacatggtattaca---cttgtgcagAAGAAGCAAAATACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAGGTTAATAACTCTGGC

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 11
-ttgg--gttttacttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG
 || |  | |    |  | | | || ||| ||  |   | |  | ||   |||    |   |  | |||  ||     | ||| || | ||    |  |||||||||| ||  | ||||| ||| |||||||| |||| |||||| | ||||| ||||| ||||||||||| |||||||| ||| |||
tttagctgatcaggtggtttatggcatatttaattacacattacgattactttgcactaccatatgtatttgatatgaagatggtattaca---cttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG

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|110372418|gb|EC936581.1|EC936581
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|30326726|gb|CD009988.1|CD009988
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|156737328|gb|EV241442.1|EV241442
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|32249612|gb|CD715431.1|CD715431
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|30131232|gb|CB916571.1|CB916571
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|71883350|gb|DT032405.1|DT032405
EST:     GCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|32247169|gb|CD712988.1|CD712988
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|352785536|gb|FQ475539.1|FQ475539
EST:     GGGAAATCATAAACATAGGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|110395213|gb|EC960849.1|EC960849
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|29783210|gb|CB349240.2|CB349240
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|352776660|gb|FQ465458.1|FQ465458
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|30325548|gb|CD008810.1|CD008810
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|110703011|gb|EE079483.1|EE079483
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|32248621|gb|CD714440.1|CD714440
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|110378991|gb|EC944156.1|EC944156
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|352777955|gb|FQ467008.1|FQ467008
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|110371972|gb|EC936111.1|EC936111
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|156737322|gb|EV241443.1|EV241443
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|29783264|gb|CB349323.2|CB349323
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
EST: gi|30324763|gb|CD008025.1|CD008025
EST:     GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA                         AAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT
genomic: GGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGAgtaagcaagc ... gttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG
         tcttaat  putative branch site (score: 3)
           ttaattatataggaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgggttttacttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaat