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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggctatagcaaccattgacagatttacacttgatgaaaatattgggctccatggtgcttcagatcactattaattgtcttttgaattctttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT

Basic information

species Vitis vinifera
transcript Vv12s0055g00390.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G05430.1 (Glycine max), 3'ss of exon 4
taggctatagcaaccatt--gacagatttacacttgatgaaaatattgggctccatggtgcttcagatcactattaattgtcttttgaattc-tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT
  |  | |     |  ||   ||    || |   ||       ||||    || | | || || || |||  |  |||  |  |   |||    | ||  ||||||||||||| ||| |||||||||| || || || |||||||||||||| ||||||||| ||||||| ||| | ||||||||||||| ||||||||||| 
-ggtttttgattgcttttccaactagctttcttgtg-cacctttattttattcaaagatgttt-agttcagcaaaaatgttaataccaataaactgtttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCATATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC

upper sequence: Vv12s0055g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G19620.1 (Glycine max), 3'ss of exon 3
----taggctatagcaaccattgacagatttacacttgatgaaaatattgggctccatggtgcttcagatcactattaattgtcttttgaattc-tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT
    |    ||||||     || |||  | |    |         ||||    || | | || || || |||  |  |||| |  |   |||    ||||  ||||||||||||| ||| |||||||||| || || || ||||| |||||||| ||||||||| ||||||| ||| | ||||||||||||| ||||||||||| 
gcttttccatatagcttgagttcacaagtct----tgtgcacctttattttattcaaagatgttt-agttcagcaaaaattttaataccaataaactttttccagAACTTTACACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGC
















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|34415352|gb|CF414106.1|CF414106
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|110422359|gb|EC988680.1|EC988680
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|110726796|gb|EE102901.1|EE102901
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|110413954|gb|EC979773.1|EC979773
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|32272342|gb|CD721501.1|CD721501
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|32247432|gb|CD713251.1|CD713251
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|30326219|gb|CD009481.1|CD009481
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|71883301|gb|DT032356.1|DT032356
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|110408688|gb|EC974328.1|EC974328
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA
EST: gi|110370922|gb|EC934544.1|EC934544
EST:     AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAG                         AACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCCTATTCTACAA
genomic: AGGCTTTGAGTGGAGCCCAGAAGCACAGTGTATTGTGGCTGCATTTTCAGgcaagatttt ... tttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctccatggtgcttcagatcactattaattgtcttttgaattctttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT
                        tattaat  putative branch site (score: 2)
                                          ttcttttt  putative PPT
                        tattaattgtctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggctatagcaaccattgacagatttacacttgatgaaaatattgggctccatggtgcttcagatcactattaattgtcttttgaattctttttggcagAACTTTACACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - -gcaacca
- - - - - - - - - - - - - - cacttga
- - - - - - - - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - ccatggt