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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatattttcagactcatgattaataaatctaataatttgacatagtctgtgattgtaatcaaacctattgggtcttaacttggtcactaaacatgaaaaatcaatgtttcag

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA20G33380.1 (Glycine max), 5'ss of exon 11
CCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatattttcag-----actcatgattaa-taaatctaataatttgacatagtctgtgattgtaatcaaacctattgggtcttaacttggtcactaaacatgaaaaatcaatgtttcag
||| |||||  |||||||||||||| |||| || || |||||||||||  | |||||    || ||||||||||| |||||||||||||| || || |||| ||  |||  |      |  |||   ||| || ||    |||   || ||    | |  ||||  | ||| ||     ||  |   ||| |   |   ||                   
CCCTGACTTCTTAAATGCTAGAATTGATGGTTTGCCAGTCAAAGAGGTGGTTAAGGATCATAAGTGGTTGGAGGAAGAGTTCACTGAAAAGGTTCAAAAGgtaaattttgtaattagcatacatagctaaatacatggtgtaaaaagatatgtagtttccttgtgctgaaagctgacaagtaattgtttgtttgattggcag------------------
















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|34550508|gb|CF518726.1|CF518726
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|34550427|gb|CF518645.1|CF518645
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|110725848|gb|EE102783.1|EE102783
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|30137894|gb|CB923232.1|CB923232
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|351040604|gb|FQ438148.1|FQ438148
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|110381192|gb|EC946513.1|EC946513
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|28963316|gb|CB342349.1|CB342349
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGGGGTGGTGTGTTGATTCAGAAATNNNNNNNATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|33402579|gb|CF208206.1|CF208206
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|110367124|gb|EC931047.1|EC931047
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|110392317|gb|EC957652.1|EC957652
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|351046814|gb|FQ454424.1|FQ454424
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|349811478|gb|FQ409474.1|FQ409474
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCCGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|32245213|gb|CD711032.1|CD711032
EST:     TCAAGGACATCAAATGGTGGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|18458671|gb|BM436949.1|BM436949
EST:     GTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: GTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|110393853|gb|EC959389.1|EC959389
EST:     TCTAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT
EST: gi|18458011|gb|BM436289.1|BM436289
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGAGNGTGGTGTGTTGATTCAGAA-TGGNGGGAGATCTTCTGCTGCATCAA
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAG-GTGGTGTGTTGATTCAGAAATGG-GGGAGATCTTCTGCTGCATCAA
EST: gi|29785366|gb|CB342287.2|CB342287
EST:     TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAG                         AGGGGTGGTGTGTTGATTCAGAAATNNNNNNNATCTTCTGCTGCATCAACT
genomic: TCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatatttt ... aatgtttcagAGAGGTGGTGTGTTGATTCAGAAATGGGGGAGATCTTCTGCTGCATCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGAAGgcaatattttcagactcatgattaataaatctaataatttgacatagtctgtgattgtaatcaaacctattgggtcttaacttggtcactaaacatgaaaaatcaatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG