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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG

Basic information

species Vitis vinifera
transcript Vv05s0020g04720.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 4
--------cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
         | || ||| |  || | | | |  ||| |||| ||| ||  ||| |    ||| | |  |  | | |||| |  ||||| |||  | ||||| |||||||||||||| | |||||||||  | ||||||||| |||||||||||||||| ||  |||||||| |||||||||||
gcactagttccatgttgctctagtt-tcctttcttccttttatttattgactttt----ttggttcagtcatgaactttaaa-attat-tgtaat-tgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 4
--cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatc--tttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
   |||  | | ||  | | |   |   | | ||  |||| ||||||   |  ||  || ||  |||||    || |  ||||| |||  | ||||| |||||||||||||| |  ||||||||  | ||||| ||| |||||||||||||||| ||  |||||||| |||||||||||
gctctagttcgattttgctcttgtttcctttcttccttttgtttctt--aacttttttggttcagtcatgaactttaaaattat-tgtaat-tgtaatctgcagATTAGTAGTCGAAATTTGGACAGAGTTCGAAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 5
cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
                   |    |  ||   || ||| ||    |      || | |  || ||| ||   ||  |||  | || |||      || |||||||||||| |||||||||| | ||||| |||||||||||||| |||||  | ||||| |||||||||||||||
-------------------gtaggtacctcaatgatttattatcaccag---tgatccagttttcaactac-atttttacat-tcgtct------tgtagATTAGTAGCCGTAATTTGGATAGAGTTCGGAAATTGAAGAGTGCCATGACTCGGTTGACAGCTCGGGTTCAAAAG

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 4
cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttg-ctgcttttgtcatc-tttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
             || ||  |       || ||||  |   |  ||| |      || | |||  |  | ||   ||  |  |   | | |  |   || |||| ||||||| ||| |||||  | |||||||||||||||||||| |||||  | ||||| |||||||| ||||||
-----------gtagcta-actcagcaattattgtcatcactgatctaattccaacttcatttaactccattcagtcgatgagaaccgttt-cattttgtagATAAGTAGCCGTAACTTGGAAAGAGTTCGTAAATTGAAGAGTGCCATGACCCGTTTGACAGCTCGGGTCCAAAAG

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|161719350|gb|FC068970.1|FC068970
EST:     CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAG                         ATTAGTAGCCTTAATTTGGATCGGGTTCGTAAA
genomic: CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAGgtgagtagga ... taaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAA
EST: gi|161717315|gb|FC065266.1|FC065266
EST:     CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAG                         ATTAGTAGCCTTTATTTGGATCGGG
genomic: CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAGgtgagtagga ... taaactgcagATTAGTAGCCTTAATTTGGATCGGG
EST: gi|71857515|gb|DT006570.1|DT006570
EST:     CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAG                         ATTAGTAGCCTTAATTTGGATC
genomic: CAGAACTGGAAACTGCTGCTTATCCAGCTTTGGATCAGCTTACGTCCAAGgtgagtagga ... taaactgcagATTAGTAGCCTTAATTTGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
                      ctttgat  putative branch site (score: 5)
                                      tcttctgt  putative PPT
                           atcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - tgcctct
- - - - - - - - - - - - - - - - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - - - - - -gcttgct