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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgttgatctttttcagataactgttactttgttccttgtgggaaagtttgtcttaccctttttttttgacttgcaaattatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCTTTGGTGGTCAAAGAAAGTTTTTCAAAGATTGATGAATCTAAAGATACTG

Basic information

species Vitis vinifera
transcript Vv19s0090g01190.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G46390.2 (Glycine max), 3'ss of exon 4
gtttgtttgttgatctttttcagataactgttactttgttccttgtgggaaagtttgtcttaccctttttttttgacttgcaaattatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCTTTGGTGGTCAAAGAAAGTTTTTCAAAGATTGATGAATCTAAAGATACTG
                        ||| | | |     ||  |       || ||  ||||   ||||  | |         || ||||||| ||||||||||||| || ||| | |||||||| |||||| |||||||||| || | ||| |  |  |||| ||||||||| ||||||   ||||  ||  |||
---------------------gtctaaatttgatcccttttgtcccaaataatttcctcttcaactttgctctgagtgctttaagtatgctgtagAATTTTGCAAAGAGTTTACTAGATGTTGCGGACAATTTGGGAAGAGCTTCCTCGGTTGCAACGGAAAATTTTTCAAAAATTGATACGTCTAGTGACTCTG

upper sequence: Vv19s0090g01190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G26780.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtttgttgatctttttcagataactgt-tactttgttccttgtgggaaagtttgtcttaccctttttttttgacttgcaaattatgc-tgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCTTTGGTGGTCAAAGAAAGTTTTTCAAAGATTGATGAATCTAAAGATACTG
        |||  |||||   |  |   | |  |  || |   |  |   | ||||| ||| |    | | | || |||    |  ||||  |||||||||||||||| ||| |||||||||| || || ||||| |||||||| |||| ||| ||||||||||| || |||||| ||||    ||  ||||| |||
--------gttagtctttaagaacttggtttgcagcttttgtttcatataatagttt-tctgaaatatatatattcact----atatatgtatgcagAATTTTGCAAAGAGCCTATTGGATGTGGCGGATAATCTTGGAAGAGCTTCTTCGGTTGTCAAAGAAAGCTTCTCAAAGCTTGACACCTCAGAAGATTCTG
















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|351056213|gb|FQ453675.1|FQ453675
EST:     TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAG                         AATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
genomic: TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAGgtttgtttgt ... tatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
EST: gi|349812967|gb|FQ411207.1|FQ411207
EST:     TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAG                         AATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
genomic: TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAGgtttgtttgt ... tatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
EST: gi|351054173|gb|FQ450255.1|FQ450255
EST:     TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAG                         AATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAA
genomic: TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAGgtttgtttgt ... tatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAA
EST: gi|351053831|gb|FQ441597.1|FQ441597
EST:     TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAG                         AATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGAAAGAGCCTCT
genomic: TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAGgtttgtttgt ... tatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
EST: gi|351056684|gb|FQ443311.1|FQ443311
EST:     TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAG                         AATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT
genomic: TGGAGAGGGCAAGACGCGAAGCAGAGAACTCCAAGAAGTTTGCCATACAGgtttgtttgt ... tatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtgggaaagtttgtcttaccctttttttttgacttgcaaattatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCTTTGGTGGTCAAAGAAAGTTTTTCAAAGATTGATGAATCTAAAGATACTG
                              ttttgac  putative branch site (score: 3)
                         tttttttttgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgttgatctttttcagataactgttactttgttccttgtgggaaagtttgtcttaccctttttttttgacttgcaaattatgctgcagAATTTTGCAAAAAGCTTATTGGATGTTGCAGACAATCTGGGAAGAGCCTCTTTGGTGGTCAAAGAAAGTTTTTCAAAGATTGATGAATCTAAAGATACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA