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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcatgactgaaacttcacttgtgtgaatcaatggaaacttctcagttgtcttacctctgggttgtttacag

Basic information

species Vitis vinifera
transcript Vv02s0025g02640.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G09680.2 (Glycine max), 5'ss of exon 6
ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagt-tcatgactgaaacttcacttgtgtgaatcaa-tggaaacttctca-gttgtcttacctctgggttgtttacag
|||||||||| ||||||||||| ||||| ||||| |||||||||||| |||||||||| || || || || |||||  | |||| | || |||| ||| ||| | ||  | |    ||||      |||||||| |  ||  || |||  || |   |            || |||
ATTTTGAAGACATGAGTTGTGATATGGTGTATGGCCAAGTCCCACCTACATTTGAAGAAGACCCTGTTTCAAAACAAGCTTGTTATGCGAATATATgtgagtatgattcccgggtgttca-----atgaatcaaataaaagattttcatattttaacaaggtaataacactttcag

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G10340.1 (Glycine max), 5'ss of exon 6
ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcatgactgaaac-ttcacttgtgtgaatcaatggaaacttctcagttgtcttacctctgggttgtttacag
|||||||||||||||||||||| ||||| ||||| |||  ||||||| ||||||||||||| || || || ||||| || || | | ||||||| |||||||    | |       |||| |      |||||    | | ||     || |   |            || |||
ATTTTGAAGATATGAGTTGTGATATGGTGTATGGCCAATCCCCACCTACATTTGAAGAGGACCCTGTTTCAAAACAACCTTGCTATGCGGATATATgtaagtatgagcccctggtgttcaatgaatcaaatcac---agattttcatattttaacaaggtaataacactttcag
















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|110384986|gb|EC949461.1|EC949461
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCC
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCC
EST: gi|110379290|gb|EC944475.1|EC944475
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
EST: gi|110376860|gb|EC941936.1|EC941936
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
EST: gi|110422103|gb|EC988415.1|EC988415
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
EST: gi|110372636|gb|EC936820.1|EC936820
EST:     TCCATTTGAAGAGGATCCAGTGTCCCAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
EST: gi|110429787|gb|EC996293.1|EC996293
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
EST: gi|27755371|gb|CB036126.1|CB036126
EST:     TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT                         GTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG
genomic: TCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcat ... ttgtttacagGTTCCATGGCAAATCCCAACTCCAGCATCTGTCATAAACTACAAGCCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCTgtaagttcatgactgaaacttcacttgtgtgaatcaatggaaacttctcagttgtcttacctctgggttgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT