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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTTGGGACAAGTGGATCGCTTGATGGACAGCAAAGATTAGTTGTGAAGGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtatttgattatgatttgatttattgtgttaatgatctataagagatggatattctctaagaggaataccagtaatgcatgaatacacattcagaa...

Basic information

species Vitis vinifera
transcript Vv06s0004g08180.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA14G38600.1 (Glycine max), 5'ss of exon 8
GAACTTGGGACAAGTGGATCGCTTGATGGACAGCAAAGATTAGTTGTGAAGGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtatttgattatgatttgatttattgtgttaatgatctataagagatggatattctctaagaggaataccagtaatgcatgaatacacattcagaa----
||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||| |||||||||||||| |||||||| ||  ||||| ||||| |||||||||||||| || | || ||||    ||| ||  |  ||   || ||| || |        |  | | | ||| |  ||  | | |     ||   |     
GAATTGGGTACAAGTGGCTCCCTTGATGGACAGCAGAGATTGGTTGTAAAGGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtatttg-ttgt-atgtgataatctgttttggtt-tcagaaatagaaggttggaaaagtatggaagttcca-tgttgagttagttgttgtttgtattgct

upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA02G40310.1 (Glycine max), 5'ss of exon 8
GAACTTGGGACAAGTGGATCGCTTGATGGACAGCAAAGATTAGTTGTGAAGGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtatttgattatgatttgatttattgtgttaatgatctataag-agatggatattctctaagaggaataccagtaatgcatgaatacacattcagaa----------------------------------------------------------------------------
||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||| |||||||||||||| |||||||| ||  ||||| ||||| |||||||||||||| || | || |    || | ||||   | |  | ||  || | |  |       |   || |   ||    |||   ||  || |  | ||                                                                            
GAATTGGGTACAAGTGGCTCCCTTGATGGACAGCAGAGATTGGTTGTAAAGGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtatttgttttttatatttgataatctgttgtggtttcagaaataggttggaaagtatggaacagagtg--agcctagcagacatgaacttcaaaaattctcccttggctattgcttttctgtctattttcgggccatcagttgaagttgatatacctctttgtttttttcag
















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|22008615|gb|BQ793649.1|BQ793649
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|26258607|gb|CA809670.1|CA809670
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGAGTGCAAAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|34548729|gb|CF516961.1|CF516961
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAGAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|26257846|gb|CA808909.1|CA808909
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|110412214|gb|EC977955.1|EC977955
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCAGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|34548647|gb|CF516879.1|CF516879
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAGAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|352785931|gb|FQ475934.1|FQ475934
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|110363156|gb|EC926727.1|EC926727
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCAGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
EST: gi|32458044|gb|CD799218.1|CD799218
EST:     GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCA                         ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA
genomic: GGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtattt ... gtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTTGGGACAAGTGGATCGCTTGATGGACAGCAAAGATTAGTTGTGAAGGGAAGATTTGCACCAAAGAATTTTGAAGGGATCTTGCGAAGATATATCAgtaagtatttgattatgatttgatttattgtgttaatgatctataagagatggatattctctaagaggaataccagtaatgcatgaatacacattcagaa

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataca