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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgacgaatcattaattaatgatcggatggaatggaaagtagttacaatttcttatccacagtgatgcagttctgatattgccctattgctgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTCTTCAGAAAGTG

Basic information

species Glycine max
transcript GLYMA02G46200.1
intron # 5
splice site 3'
intron type U2

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|23064235|gb|BU579008.1|BU579008
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|13481968|gb|BG511311.1|BG511311
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|193410849|gb|FK378936.1|FK378936
EST:     TTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGGTCTATTTT
genomic: TTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGC-GTCTATTTT
EST: gi|13251924|gb|BG362827.1|BG362827
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|213615236|gb|DB965044.1|DB965044
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|213616511|gb|DB965709.1|DB965709
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|209721887|gb|BW680046.1|BW680046
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|193557293|gb|FK511606.1|FK511606
EST:     GAAGCTGGATTAATTCAAAGACCTAATAGAG                         GGTGGTCATTCATCCAGAGGCAA
genomic: GAAGCTGGATTAATTCAAAG-CCTA-T-GAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAA
EST: gi|120491274|gb|EH219441.1|EH219441
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|208079599|gb|GD875787.1|GD875787
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|209726695|gb|BW672449.1|BW672449
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|298170020|gb|HO018644.1|HO018644
EST:     GAAGCTGGATTAATTCAGAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTCTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|7924360|gb|AW830386.1|AW830386
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
EST: gi|298174924|gb|HO014841.1|HO014841
EST:     GAAGCTGGATTAATTCAAAGCCTATGAG                         GGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC
genomic: GAAGCTGGATTAATTCAAAGCCTATGAGgtttgtggca ... tgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttcttatccacagtgatgcagttctgatattgccctattgctgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTCTTCAGAAAGTG
                         ttctgat  putative branch site (score: 3)
                                            ctgctct  putative PPT
                            tgatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgacgaatcattaattaatgatcggatggaatggaaagtagttacaatttcttatccacagtgatgcagttctgatattgccctattgctgctctgtagGGTGGTCATTCATCCAGAGGCAACTGTTCGAACTTGGGGGCGTCTATTTTCTTCAGAAAGTG

- - - - - - - - - - - - ggatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgccct