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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgtcaattgcaaagtggttgtactatgttatgtttcttcatttcatatttaacattgttatccaacctgaactttgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTGCCTCCCAATAGGGAAAGCCAAG

Basic information

species Vitis vinifera
transcript Vv01s0146g00310.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtcgtcaattgcaa----agtggttgtactatgttatgtttcttcatttcatatttaacattgttatccaacctgaactttgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTGCCTCCCAATAGGGAAAGCCAAG
|||||| || | |   ||    |||  ||| |     |||          | ||||||    || |     |  |  |  | ||  |  | ||| ||||||||||| |||||||| |||| |||||  |||||||| ||||| || || || ||||| |||||||||
gtaagtagt-attcctaatttgagttcttgcatgtgattagagcctacggtctcatat----cagtacctccttaaattgatttcatcatgcagATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG
















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|351043256|gb|FQ443977.1|FQ443977
EST:     CTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAAATGA-TTGCT                         GTATGGTGA-TCCTTCCCTATCTCA
genomic: CTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAA-TGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCA
EST: gi|351034261|gb|FQ448058.1|FQ448058
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|351023552|gb|FQ432935.1|FQ432935
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCA
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCA
EST: gi|351014802|gb|FQ438002.1|FQ438002
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|77587570|gb|DV222950.1|DV222950
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|77577175|gb|DV217284.1|DV217284
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110378632|gb|EC943772.1|EC943772
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|351029889|gb|FQ427729.1|FQ427729
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|349828778|gb|FQ418513.1|FQ418513
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110371230|gb|EC935083.1|EC935083
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|351017574|gb|FQ435927.1|FQ435927
EST:     CTGCTATAAAAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTTGCT                         GTATGGTGAATCTTTCCCTATCTCACCAGAAGT
genomic: CTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTT-GCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGT
EST: gi|110685369|gb|EE062030.1|EE062030
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAA-TGAGTTGCT                         GTATGGTGAATCTTTCCCTGTCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110365136|gb|EC928913.1|EC928913
EST:     CTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTTGAAA-TGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: CTGCTATAAGAGACCCTGATCCTGTTATTTTCCTT-GAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|349818046|gb|FQ408821.1|FQ408821
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCT
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCT
EST: gi|110713083|gb|EE088693.1|EE088693
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTGTCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110387837|gb|EC952535.1|EC952535
EST:     CTGCTATAAGAGACCCTGATCCTG-TATTTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: CTGCTATAAGAGACCCTGATCCTGTTA-TTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|351015619|gb|FQ427104.1|FQ427104
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAACGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|351028389|gb|FQ427285.1|FQ427285
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|349826357|gb|FQ417854.1|FQ417854
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|161715045|gb|FC064252.1|FC064252
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATT
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATT
EST: gi|351029935|gb|FQ427775.1|FQ427775
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTT
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTT-
EST: gi|110398758|gb|EC965232.1|EC965232
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110718877|gb|EE096214.1|EE096214
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTGTCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
EST: gi|110702444|gb|EE081168.1|EE081168
EST:     GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCT                         GTATGGTGAATCTTTCCCTGTCTCAGCAGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATAAGAGACCCTGATCCTGTTATTTTCCTTGAAAATGAGTTGCTgtaagtcgtc ... tgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcttcatttcatatttaacattgttatccaacctgaactttgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTGCCTCCCAATAGGGAAAGCCAAG
                 atttaac  putative branch site (score: 3)
          atttcatatttaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgtcaattgcaaagtggttgtactatgttatgtttcttcatttcatatttaacattgttatccaacctgaactttgtgcttcagGTATGGTGAATCTTTCCCTATCTCAGCAGAAGTTCTTGATTCCAGTTTTTGCCTCCCAATAGGGAAAGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT