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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAAATGGGATCCCAAGTGTTGGTTCCTTTCCGAGGTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaatggtgatttattcattgattcaaattttccatttgtgtgacttggtgggaacagtagtttggctggtatttccttttaatttagactttttgactgatactatcag

Basic information

species Vitis vinifera
transcript Vv07s0005g04440.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G18950.1 (Glycine max), 5'ss of exon 4
CTAAAATGGGATCCCAAGTGTTGGTTCCTTTCCGAGGTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaatggtgattt---attcattgattcaaatttt--ccatttgtgtgacttggtgggaacagtagtttggctggtatt-tccttttaatttagactttttgactgatactatcag------------------------
||||||||||||| |||||  | |||||||||||||| ||||| |||  ||  |||||||| ||||||||||| ||||| ||||||||||   | ||  || |||   ||   | || ||   | ||  |   |  |     |||||  |||  | |   |   | ||  | |   | |   |||    | |   ||  |  |   |                         
CTAAAATGGGATCTCAAGTCCTAGTTCCTTTCCGAGGCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaagataatgtttttatatgtgtagagtcctctcttgcctcctctttctttttggtcagaatggaaaggttaatagtgctatgtgtgtggattatttctatctgctatttgtgctaaccttccagtgattaatatgcccag

upper sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G20360.1 (Arabidopsis thaliana), 5'ss of exon 4
CTAAAATGGGATCCCAAGTGTTGGTTCCTTTCCGAGGTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaatggtgattta-ttcattgattc--aaattttccatttgtgtgac-ttggtgggaacagtagtttggctggtatttccttttaatttagactttttgactgatactatcag
||||||||||||| |||||| | |||||||||||||| || ||||| |||| ||| ||||| || |||||||| |||||||||||||||   ||     | |||||    | || ||   |   | | ||        || |   |   || |    |      | |       ||| || |    || ||| |||    |  |||
CTAAAATGGGATCACAAGTGCTTGTTCCTTTCCGAGGCTCAGAGGACTCTCCTCGACATCTCAAGTTGATGGGAGATTTAGGACAGgtaatgtattcttttatttaacataatgctttcgagggtatgcaacaaaaaaacatctttacaaaaaactatgcattggatcggcaaatttgatgtgtgtttgttgcctgtatattccag
















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|161719785|gb|FC066692.1|FC066692
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTT-GGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|161720302|gb|FC071155.1|FC071155
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|161719288|gb|FC068264.1|FC068264
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|77580795|gb|DV219305.1|DV219305
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|110424142|gb|EC990498.1|EC990498
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATACAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|71864241|gb|DT013296.1|DT013296
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
EST: gi|161718481|gb|FC066331.1|FC066331
EST:     GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAG                         ATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA
genomic: GTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaa ... atactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAAAATGGGATCCCAAGTGTTGGTTCCTTTCCGAGGTTCTGAGGATTCTCATCGTCATCTTAAATTGATGGGTGATTTAGGACAGgtagaataaatggtgatttattcattgattcaaattttccatttgtgtgacttggtgggaacagtagtttggctggtatttccttttaatttagactttttgactgatactatcag

- - - - - - - - - - - - - - - - - - - -  GAGGAT