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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataaaagtattgagttaactcctagcttgttacttaatcaattaccttttagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG

Basic information

species Glycine max
transcript GLYMA08G22740.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtataaaagtattgagttaactcctagctt----gttacttaa-tcaattaccttttagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG
       |||   | |  || ||  | | ||  |    | |  |||| ||||||| ||| |   ||||   |||    |||     |||| |||||| | |||||||||||||||||||||||||   ||||    | ||| ||||| | |||  ||||||| || |
------gtaagtttctctagctattttcaagtgttgaggctctttaactcaattaacttcttacaaaact-tttttggatt-----agGGTGAAAAGTTGAAACTTTTCTATAATCCAGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG
















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|22540175|gb|BU090018.1|BU090018
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|209725498|gb|BW677795.1|BW677795
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|17519381|gb|BM188423.1|BM188423
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|17400692|gb|BM177474.1|BM177474
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|10232087|gb|BE800975.1|BE800975
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|20448322|gb|BQ252446.1|BQ252446
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|151400172|gb|EV269986.1|EV269986
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|16105597|gb|BI893337.1|BI893337
EST:     GGAGGGCTGCTGTCTATTGGAAA-CCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT
EST: gi|213608233|gb|DB970830.1|DB970830
EST:     GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA                         GGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAGCTCAACTTGTCCCT
genomic: GGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCAgtaagtataa ... attttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttgttacttaatcaattaccttttagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG
         acttaat  putative branch site (score: 4)
           ttaatcaattaccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtataaaagtattgagttaactcctagcttgttacttaatcaattaccttttagtaaaaaaatttacaaattttggcagGGAGAAAAGCTAAAACTTTTCTATAATCCAGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA