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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgtagttctttatttttaatcataactgcagtttcaacaactcattcaattttgctagcaataacttttggtgatcaataatgcag

Basic information

species Glycine max
transcript GLYMA02G43550.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43550.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0059g01400.t01 (Vitis vinifera), 5'ss of exon 3
GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgtagttctttatttttaatcata-actgcagtttcaaca--actcatt--caattttgctagcaataac-ttttggtgatcaataatgcag
|||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||      ||  ||| |   ||  || ||   |  | ||  | ||    |  ||  ||||||||||  ||    | ||||     |     ||| ||
GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaataca-agcgcttcaacatttttcttatggtctaattagagcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag
















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|192327904|gb|FK022127.1|FK022127
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|9985819|gb|BE660046.1|BE660046
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|298182544|gb|HO031279.1|HO031279
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|21994307|gb|BQ785835.1|BQ785835
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|20813502|gb|BQ297980.1|BQ297980
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|7926296|gb|AW832322.1|AW832322
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTGAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
EST: gi|20498278|gb|BQ273208.1|BQ273208
EST:     TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG
genomic: TGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgta ... aataatgcagATGTCAGGAACCACCCAGTTATAATTCACTGTAAGCGTGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgtagttctttatttttaatcataactgcagtttcaacaactcattcaattttgctagcaataacttttggtgatcaataatgcag

- - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - -  TGAAGC