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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaagctaatgtcccctcaaaggtcaaggccgtgagatgttggctgaaggtaaatgttgatatgtagtgccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG

Basic information

species Vitis vinifera
transcript Vv13s0064g01360.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G00580.1 (Glycine max), 3'ss of exon 12
ttgaaagctaatgtcccctcaaaggtcaaggccgtgagatgttgg-ctgaaggtaaatgttgatatgtagtg--ccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
  |   |     ||    |  | |  ||   ||||    | ||   ||     ||  ||  | |||| || |    | | || ||||  ||| | || | ||||  | |||  ||| || ||  ||||||| ||||||||||||||||| |||||||| ||| |||||||||||||||||||||||||||||| |
--gggggggtgggtggggtggatgcacacc-ccgtctcttatttctcttgccttaggtgaagctatggagaggttgactgatttatgtttttaacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG

upper sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G42640.1 (Glycine max), 3'ss of exon 12
ttgaaagctaatgtcccctcaa-aggtcaaggccgtgagatgttggctgaaggtaaatgttgatatg-tagtgccattaatgtatgcat---tttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
       |||   | |  |  | |  |            ||  |||  |||   ||||    ||| | | |    ||| |  | | |||   | || || ||||||  | ||| ||||||||||| ||||||| |||||||||||||| || |||||||| ||| || | ||||||||||||||||||||||||| |
----tgactatctttctattgataaatttgatttaatcaattatgggagaaaa-aaatacaaatagggttgactgattcacatttacatgtatgtacatttgcagGGATTGACAACAATGAAACTATAAAGGTTTATAGAAGTGGTGGTGCAGATCCTGATGGAGATAATCCTGGTGATCTTTATGTTACTATCAAG

upper sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G16150.1 (Glycine max), 3'ss of exon 12
ttgaaagctaatgtcccctcaaaggtcaaggccgtgagatgttggctgaaggtaaatgttgatatgtagtgccattaatgtatgcat---tttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
 |||       | ||   ||| |  |            ||  |||  |||    |      |   ||      ||| |  | | |||   |||| || ||||||  | ||| ||||||||||| ||||||| |||||||||||||| || |||||||| ||| || | |||||||||||||||||||| |||| |
-tgactatc--tttctattcataaatttgatttaatcaattatgggagaaaaagagacaaaaagggttcacttattcacttttacatgtatttacatttgcagGGATTGACAACAATGAAACTATAAAGGTTTATAGAAGTGGTGGTGCAGATCCTGATGGAGATAATCCTGGTGATCTTTATGTTACCATCAAG

upper sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G36820.1 (Glycine max), 3'ss of exon 12
ttgaaagctaatgtcccctcaaaggtcaaggccgtg-------agatgttggctgaaggtaaatgttgatatgtagtgccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
        |  | | |       ||  | |  | |          || |    |     ||| || |     |  ||   | | || ||||  ||| | || | ||||  | |||  ||| || ||  ||||||| | ||||||||||||||| |||||||| ||| |||| ||||||||||||||||||||||||| |
-------ttctttttctgggggggggtatgcacatcccttctcttatttctcttcgccttaattgctatggagaggtttgactgatttatgtttttgacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTTTAGAAGTGGTGGAGCAGATCCTGATGGAGATCACCCTGGTGATCTTTATGTTACTATCAAG

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|32271787|gb|CD720946.1|CD720946
EST:     AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAG                         GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
genomic: AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAGgtattcttac ... atatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
EST: gi|32267592|gb|CD716555.1|CD716555
EST:     AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAG                         GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
genomic: AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAGgtattcttac ... atatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
EST: gi|32248657|gb|CD714476.1|CD714476
EST:     AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAG                         GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
genomic: AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAGgtattcttac ... atatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
EST: gi|32272152|gb|CD721311.1|CD721311
EST:     AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAG                         GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
genomic: AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAGgtattcttac ... atatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
EST: gi|32268945|gb|CD718104.1|CD718104
EST:     AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAG                         GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC
genomic: AGATCGAGTGGTAAGAGGATCAAAGTCAGTCAAGTTGGATATTATGCCAGgtattcttac ... atatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaggtaaatgttgatatgtagtgccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
                           cattaat  putative branch site (score: 3)
                            attaatgtatgcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaagctaatgtcccctcaaaggtcaaggccgtgagatgttggctgaaggtaaatgttgatatgtagtgccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - gctaatg
- - - - - - -tcccctc
- - - - - - - - - - - - - caaggcc
- - - - - - - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - -aggtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgca