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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttgtgcttttataaacttcattctatatttgaagctcctttgatctaataatcggcttataacaattatcatttgtaatttatgtataatttcatatgttatgctctgtttcatctccaattgcctattgcag

Basic information

species Vitis vinifera
transcript Vv17s0000g01370.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G03380.1 (Glycine max), 5'ss of exon 5
AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttgtgcttttataaacttcattctatatttgaagc------tcctttgatct------aataatcggcttataacaattatcat----ttgtaatttatgtataatttcatatgttatgctctgtttcatctccaattg-cctattgcag
|||||||  |||||| ||||||||||||| ||||| ||||||||||| | ||||    |    | ||   |  ||||| |      ||| | |   |      ||||  | | || |   | |  |||     ||||| |||   |  ||| | || |  |   || |||||    |    |||  ||| |  ||
AAATCCAGGACTGGGAATCCTTTGGAGACAAAGTACCCgtaagtgttttcctttgtccattcacttttgttgattgaaaccttaaatccataggcttgttttaaatagacagattcttttattgctcaagttattgtatttttcatcaaatgtgatcttgttgactgtgtttttctttttgttggtctactttag

upper sequence: Vv17s0000g01370.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G13950.1 (Glycine max), 5'ss of exon 4
AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttgtgcttttataaacttcattctatatttgaagctcctttgatctaataatcggcttataaca--attatcatttgtaat-----ttatgtataatttcata-tgttatgctctgtttcatctccaattgcctattgcag
|||||||  |||||| |||||||| |||| ||||| ||||||||||||||  |||      |||| | | | ||    |   | || |||  |   | |  ||| |     ||| |  |||| | |     || ||| |   || ||| |||  |        | || |  | ||    |||    
AAATCCAGGACTGGGAATCCTTTGAAGACAAAGTACCCgtaagtgttgtgtcttttgtccattcacttt-tgttgattgaaaccttaatcataggtttgttttaaagagagattctgttttgcattgaatcttctgtgtgccttaataatgtccttgctcaagttat-tgtattttttcattag--
















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|349828801|gb|FQ419134.1|FQ419134
EST:     AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCC                         TTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
genomic: AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttg ... cctattgcagTTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
EST: gi|351016978|gb|FQ424405.1|FQ424405
EST:     AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCC                         TTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
genomic: AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttg ... cctattgcagTTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
EST: gi|122692257|gb|EC996717.1|EC996717
EST:     AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCC                         TTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
genomic: AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttg ... cctattgcagTTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
EST: gi|352798795|gb|FQ478430.1|FQ478430
EST:     AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCC                         TTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC
genomic: AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttg ... cctattgcagTTATGTTTGTCATGCTGAAGTCAACGCCATCCTAAACACAAACCATGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATCCAAAACTGGGGATCCTTTGGAGACGAAGTATCCgtaagtgttgtgcttttataaacttcattctatatttgaagctcctttgatctaataatcggcttataacaattatcatttgtaatttatgtataatttcatatgttatgctctgtttcatctccaattgcctattgcag

- - - - - - - - - -  TTGGAG
- - - - - - - - - - - TGGAGA