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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattggcaattggtgttgatagaacatttagatgatctctttaaaagttattcttctttgcctttaataattgttcaacctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC

Basic information

species Vitis vinifera
transcript Vv05s0049g00470.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G34520.2 (Glycine max), 3'ss of exon 2
tattggcaatt-ggtgttgatagaacatttagatgatctctttaaaagttattc--ttctttgcctttaataa-ttgttcaac--ctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC-----
     ||| ||  ||||| | ||         || || |  ||  ||  |||    || |||   || | ||| |  ||  |   ||  ||||| ||||| ||||||| || || ||||| |||||| |||| || |||||||| |||||||| || | |||| |||||||  | ||| || |||||||||||||||| ||     
-----gcagttcagtgtt-acagttttcaataataattttgttctaaaatatcaaattatttattttgattaaatcattttataactaactgcttctttccagtagGTGGTCCTTGACAAAGAGAAACAGGTTGCCACAGTGGACAGAGAGGTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAACGTAAG

upper sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 2
tattggcaatt-ggtgttgatagaacatttagatgatctctttaaaagttattc--ttctttgcctttaataa-ttgttcaac--ctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC
     ||| ||  ||||| | ||         || || |  ||  ||  |||    || |||   || | ||| |  ||  |   ||  ||||| ||||| ||||||| || || ||||| |||||| |||| || |||||||| |||||||| || | |||| |||||||  | ||| || |||||||||||||||| ||
-----gcagttcagtgtt-acagttttcaataataattttgttctaaaatatcaaattatttattttgattaaatcattttataactaactgcttctttccagtagGTGGTCCTTGACAAAGAGAAACAGGTTGCCACAGTGGACAGAGAGGTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAAC

upper sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G33110.2 (Glycine max), 3'ss of exon 2
---tattggcaattggtgttgatagaacatttagatgatctctttaaaagttattcttctttgcctttaataattgttcaac--ctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC
    ||   |||       ||  ||  || |   ||  | | || || | | ||| |  | |    |    |||| ||  |   ||  ||||||||||| ||||||| || || ||||| |||||| |||| || ||||| || |||||||| || | |||| |||||||  | ||| |  |||||||||||||||| ||
gcagatatccaagaaaaactg-cagttcagtcttatagttt-ttgaataataattttagtctaaaatatcaaattattttataactaactgctgctttccagTAGGTGGTCCTTGACAAAGAGAAACAGGTTGCCACAGTTGACAGAGAGGTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC

upper sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G33110.1 (Glycine max), 3'ss of exon 2
tattggcaattggtgttgatagaacatttagatgatctctttaaaagttattcttctttgcctttaataattgttcaac--ctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC
 ||   |||       ||  ||  || |   ||  | | || || | | ||| |  | |    |    |||| ||  |   ||  ||||||||||| ||||||| || || ||||| |||||| |||| || ||||| || |||||||| || | |||| |||||||  | ||| |  |||||||||||||||| ||
gatatccaagaaaaactg-cagttcagtcttatagttt-ttgaataataattttagtctaaaatatcaaattattttataactaactgctgctttccagtagGTGGTCCTTGACAAAGAGAAACAGGTTGCCACAGTTGACAGAGAGGTTGACGATGGTATTGAAACCGTGTGTCTAAACTTACCAGCAGTAATAAC

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|37185949|gb|CF605302.1|CF605302
EST:     AAATGGTAGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAG                         GTTGTGCTGGACAAGGAGAAAGAGGTGGCAACGGTGGAGAGAGAGGTGGAT
genomic: AAATGGTTGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAGgttagtccca ... tttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGAT
EST: gi|27582621|gb|CB005316.1|CB005316
EST:     AAATGGTAGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAG                         GTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGAT
genomic: AAATGGTTGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAGgttagtccca ... tttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGAT
EST: gi|161712333|gb|FC061658.1|FC061658
EST:     AAATGGTAGCTGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAG                         GTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGAT
genomic: AAATGGTTGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAGgttagtccca ... tttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattcttctttgcctttaataattgttcaacctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC
                ctttaat  putative branch site (score: 4)
                                         ctgctttct  putative PPT
                 tttaataattgttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattggcaattggtgttgatagaacatttagatgatctctttaaaagttattcttctttgcctttaataattgttcaacctggctgctgctttctagtagGTTGTGCTGGACAAGGAGAAAGAGGTGGCAACAGTGGAGAGAGAGGTGGATGGTGGTCTTGAAACTTTATGTTTGGACTTACCAGCAGTAATCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - -ggtgttg
- - - - - - - - - atagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgctg