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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttccagaaggctaatcaacagtatctacttctgaaatgcatctggaatccttttactgtatttagttttaattttattcaattttttctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGAAAAGCGGGTGTAAAATTGGCTGTTGTATCAAACTTTGATACTCGATTAA

Basic information

species Vitis vinifera
transcript Vv08s0007g05350.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G28600.1 (Glycine max), 3'ss of exon 3
--------------------ttcttccagaaggctaatcaacagtatctacttctgaaatgcatctggaatccttttactgtatttagt-tttaattttattcaattttttctgtccaaa--gGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGAAAAGCGGGTGTAAAATTGGCTGTTGTATCAAACTTTGATACTCGATTAA
                     | ||| | || |   ||    | |||||   |||| | |   |      |  || || | |   |||| ||| ||  | ||   | | |    |||| |  ||| |||||||||  ||||||||  |||||   ||||||||   ||||||||||| | ||||| ||||| |||||||| ||||||||||| ||| ||||||
gtagattacttataattaccattttctaaaatgtatat----actatctctctctgtatttttttatttttttttataatttgggtagtgtttgatagttttggctgtctatcatccatatagGCATGGCACCTCAATGATCCTGGCGCAGAAGAAGTATTCAGAGCTCTTAGAAAATCAGGTGTGAAATTAGCTGTTGTGTCAAACTTTGACACTAGATTAA

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G31340.1 (Glycine max), 3'ss of exon 3
ttcttccagaaggctaatcaacagtatctacttctgaaatgcatc-tggaatccttttactgtatttagttttaattt-----tattcaattttttctgtc--------------caaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGAAAAGCGGGTGTAAAATTGGCTGTTGTATCAAACTTTGATACTCGATTAA
       ||||  || || |  | |  |   ||||  |||  | | |    |  ||||  | |||||  || ||||||     | ||  || ||||  | |               | |||| |||||||||  |||| |||  |||||   ||||||||   ||||||||||| | ||||| ||||| |||||||| ||||||||||| ||| ||||||
----gtaagaacacttattataattgccattttctagaatatagcatactcttttttttttatatttt-ttataatttcgtagtgtttgatatttttggccgtctataatccccatatagGCATGGCACCTCAATGATACTGGTGCAGAAGAAGTATTCAGAGCTCTTAGAAAATCAGGTGTGAAATTAGCTGTTGTGTCAAACTTTGACACTAGATTAA
















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|32267815|gb|CD716974.1|CD716974
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110731628|gb|EE106216.1|EE106216
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAAGCAGAAAGAGTATTCATGTCTCTTANA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|30299817|gb|CB976611.1|CB976611
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|22014371|gb|BQ799405.1|BQ799405
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110395612|gb|EC961279.1|EC961279
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110429697|gb|EC996199.1|EC996199
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|22014482|gb|BQ799516.1|BQ799516
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|161719017|gb|FC067637.1|FC067637
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCATAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|26258618|gb|CA809681.1|CA809681
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|33403871|gb|CF209498.1|CF209498
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|22011451|gb|BQ796485.1|BQ796485
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|71871882|gb|DT020937.1|DT020937
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110725316|gb|EE101677.1|EE101677
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTANN
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110366475|gb|EC930383.1|EC930383
EST:     ACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: ACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|161712968|gb|FC062094.1|FC062094
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|33409774|gb|CF215401.1|CF215401
EST:     AGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTTTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: AGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|26264895|gb|CA815958.1|CA815958
EST:     CTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110730112|gb|EE106820.1|EE106820
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAAANAGAGTATTCATGTCTCTTAAA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110713079|gb|EE088696.1|EE088696
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAAGCAGAGAGAGTATTCATGTCTCTTANA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|71877278|gb|DT026333.1|DT026333
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|33409859|gb|CF215486.1|CF215486
EST:     TACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: TACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|294965827|gb|GW837310.1|GW837310
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCAGTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGA
EST: gi|329112330|gb|JG391798.1|JG391798
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|34320237|gb|CF372991.1|CF372991
EST:     CAGATACTCAGTACTTTGAGGAACTTTACC-CTACTATACTACTGAAGAG                         GCTTGGCACCTCTGT-ATTCCTGAGGCAGAGAGAGTATTCATGTCTCTTAG
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGA-TCCTGAGGCAGAGAGAGTATTCATGTCTCTTAG
EST: gi|26257149|gb|CA808212.1|CA808212
EST:     CCGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAG
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAG
EST: gi|110731791|gb|EE106512.1|EE106512
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110688614|gb|EE067366.1|EE067366
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAAGCAGAGAGAGTATTCATGTCTCTTANA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|294966056|gb|GW837423.1|GW837423
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAAAG                         GCTTGGCACCTCTGTGATCCTGAG
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAG
EST: gi|22014205|gb|BQ799239.1|BQ799239
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110713855|gb|EE090151.1|EE090151
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAAAAAGA-TATTCATGTCTCTTANA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|71877965|gb|DT027020.1|DT027020
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|161715593|gb|FC068349.1|FC068349
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTAT-CATGTCTCTTAGA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA
EST: gi|110712773|gb|EE088110.1|EE088110
EST:     CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAG                         GCTTGGCACCTCTGTGATCCTGANGCAGAGAGAGTATTCATGTCTCTTAAA
genomic: CAGATACTCAGTACTTTGAGGAACTTTACCACTACTATACTACTGAAGAGgtcaggttct ... ctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatccttttactgtatttagttttaattttattcaattttttctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGAAAAGCGGGTGTAAAATTGGCTGTTGTATCAAACTTTGATACTCGATTAA
                       ttttaat  putative branch site (score: 3)
                                       ttttttctgtcc  putative PPT
        ttttactgtatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttccagaaggctaatcaacagtatctacttctgaaatgcatctggaatccttttactgtatttagttttaattttattcaattttttctgtccaaagGCTTGGCACCTCTGTGATCCTGAGGCAGAGAGAGTATTCATGTCTCTTAGAAAAGCGGGTGTAAAATTGGCTGTTGTATCAAACTTTGATACTCGATTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
-tcttcca
- - - - - - - -aatcaaca
- - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - gcatctg