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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTAAGCTTGGTGAATGCAGAATCATTCTATGTGAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccctttagtgaacccacaattgttactcaataatccaactgatgaattatgcaaactgttagtacttttttttttctttatcaaaaaacaaac...

Basic information

species Vitis vinifera
transcript Vv06s0004g02050.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02050.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA13G41490.1 (Glycine max), 5'ss of exon 15
TTGTAAGCTTGGTGAATGCAGAATCATTCTATGTGAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcc------cctttagtgaacccacaattgttactcaataatccaactgatgaattatgcaaactgttagtacttttttttttctttatcaaaaaacaaac
 |||| ||||||||||||||| || ||| ||||||||||||| || ||||| | |||||| || |||||||| ||||| || |||||||| |      ||  ||      |  ||  || | |   | || | ||     | ||||||   | ||      |      | |  |||  | | ||      
CTGTAGGCTTGGTGAATGCAGGATTATTTTATGTGAAGCAGGTGCCAAGCACAAGTTGCAAAAATTGCAGCTTAATTTCCCGAGgttagttctcaaagcccctatcatttcttcagctgatcccacagaaacaaatgacgggattatgagtagtgcctaaccaaggaatctagtttcccgacaa------

upper sequence: Vv06s0004g02050.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA15G03900.1 (Glycine max), 5'ss of exon 17
TTGTAAGCTTGGTGAATGCAGAATCATTCTATGTGAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccctttagtgaacccacaattgttactcaa-taatccaactga--tgaattatgcaaactgttagtacttttttttttctttatcaaaaaacaaac---
 |||| ||||||||||||||| || ||| ||||||||||||| || ||||| |||| ||| || |||||||| ||||| || |||||||| | |       |||||  |    ||  |||  | |||| || ||    ||| | |   | | |  ||| |    ||||  | |    |  |     |   
CTGTAGGCTTGGTGAATGCAGGATTATTTTATGTGAAGCAGGTGCCAAGCACAGGTGGCAAAAATTGCAGCTTAATTTCCCGAGgttagttctca-----aaacccctatcattttttcagctgatcccacagaaacaaatgacg-ggattatgggtattgcagttttgatctgaacacgattttgcttt
















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|30136412|gb|CB921750.1|CB921750
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGATAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|110361075|gb|EC924528.1|EC924528
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|33405995|gb|CF211622.1|CF211622
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|87583901|gb|DY473272.1|DY473272
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|110362552|gb|EC926095.1|EC926095
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|110363917|gb|EC927549.1|EC927549
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|33406095|gb|CF211722.1|CF211722
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGAGATCGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|83276293|gb|DV940301.1|DV940301
EST:     TAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: TAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|110363719|gb|EC927329.1|EC927329
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC
EST: gi|30329378|gb|CD012640.1|CD012640
EST:     GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAG                         TGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGN
genomic: GAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccc ... cttgtgacagTGATGATGTAGCATTTGCACTCAAAGATGACAAGGAACTACCTTGGTTAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTAAGCTTGGTGAATGCAGAATCATTCTATGTGAAGCAGGAGCTAAGCATAGGTTGCAGAAGTTGCAGCTCAATTTTCCAAGgttagtcccctttagtgaacccacaattgttactcaataatccaactgatgaattatgcaaactgttagtacttttttttttctttatcaaaaaacaaac

- - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa