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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatggcactttcatttatagcagagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT

Basic information

species Vitis vinifera
transcript Vv09s0002g06730.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G22580.2 (Glycine max), 3'ss of exon 2
---------agaatggcactttcatttatagca-gagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT
           | ||| |  |  || |||  || ||| ||| ||    || | |||   |   |   ||||        | |||||||||| |  ||| ||| | |  |||| | |||||||||||||| |||| |||| ||||||| ||||| ||||||||||| |||| ||||||||| |||||||| ||||| ||||  || ||  |
tttcacttagcactggaaaatggatatatttcaagagctgtggaatactttacatttacgtatctgctgct--------atttaccttttttt--ttggtttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCT

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G03510.1 (Glycine max), 3'ss of exon 3
-------agaatggcactttcatttatagcagagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT
       ||    | |   | | |  |   |||| ||| ||    || | |||   ||  |   ||||  ||     |  |  ||||| |  ||| ||| | |  |||| |||||||||||||||| |||| |||| ||||||| ||||| ||||||||||  |||| ||||||||| |||||||| ||||| ||||  || ||| |
ttcacgtagtgctggaaaatgaatatttcaagagctgtggagtactttacatttacgaatctgctgctattt-----accattttttttt--ttggtttttctctagTGTCAGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCTCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGCCT

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G01150.1 (Glycine max), 3'ss of exon 4
-agaatggcactttcatttatagcagagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT
    || |   |||||   | ||| ||    |  |  || ||    | || |     || |        ||  ||  |  |  |  ||  ||| | |  |||| |||||||||||||||| |||| |||| ||||||| ||||| ||||||||||| |||| ||| || || ||||| ||||| || ||||  || || ||
acatattgtgatttcacccagagctgaaaaatgaatgttctagagctattaagtgttttacatcaacagta-ctatttactaatattttgtttttctccagTGTCAGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAACGTCTTTTCCTGGATAAATATGGAAGAATTTGTTT

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|37190396|gb|CF609745.1|CF609745
EST:     AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT                         TGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA
genomic: AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTTgtaagtatat ... ttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA
EST: gi|352777162|gb|FQ474469.1|FQ474469
EST:     AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT                         TGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA
genomic: AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTTgtaagtatat ... ttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA
EST: gi|37190163|gb|CF609512.1|CF609512
EST:     AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT                         TGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA
genomic: AGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTTgtaagtatat ... ttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT
                                            tttcttt  CT-rich tract
               tgattttttaattacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatggcactttcatttatagcagagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT

- aatggca
- - - - - - - - - - - - - - tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - cccattg