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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accattgccaataagcatatccattggtaaaaagtattaacaggtaatgcattatcccttttatatgctgttatttaattttgacacattttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGATGTCGTATCTTCGAATCTAAG

Basic information

species Glycine max
transcript GLYMA17G03990.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 9
accattgccaataagcatatccattggtaaaaagtattaacaggtaatgcattatcccttttatatgctgttatttaattttgacacattttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGATGTCGTATCTTCGAATCTAAG
            |||  ||    |  ||  ||  |  |      |  | |  |  | |||    ||  ||   | |  |  | ||     |  |   ||||||||||| || || ||||| ||||||  ||||||||||| |||||||||    ||   ||| ||  ||||
---------gtaaagtgtacaactctgtggaatattgtgttttttcttaccctgactcttaataataatg--gtctgctgcttacgg---tcatcaacagAGAGCTGCACACGTTTATTCCGAAGCCCGGAGGGTTCATGGTTTCAAGGACACAGTTAATTCAAACTTAAG
















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|4396496|gb|AI495493.1|AI495493
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|14205721|gb|BG839399.1|BG839399
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTSCTCATGTGTATTCAGAKSCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|41145398|gb|CK605609.1|CK605609
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|14205748|gb|BG839426.1|BG839426
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|58019629|gb|CX706371.1|CX706371
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|15203268|gb|BI426036.1|BI426036
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|26048836|gb|CA785289.1|CA785289
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|207698661|gb|GD679290.1|GD679290
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
EST: gi|58019308|gb|CX706050.1|CX706050
EST:     CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAG                         AGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT
genomic: CAGCTTATTTAGAAGTGTTAAAAGTTGCAAAGCAATACAAGTTGCATCAGgttatttctt ... ttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcattatcccttttatatgctgttatttaattttgacacattttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGATGTCGTATCTTCGAATCTAAG
                                 ttttgac  putative branch site (score: 3)
                                           ttttgtttcc  putative PPT
             ttttatatgctgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accattgccaataagcatatccattggtaaaaagtattaacaggtaatgcattatcccttttatatgctgttatttaattttgacacattttgtttccagAGAGCTGCTCATGTGTATTCAGAAGCCAAGAGGGTTCATGCTTTCAAGGATGTCGTATCTTCGAATCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- cattgcc
- - - - - - - - - - - - -ggtaaaaa
- - - - - - - - - - - - - - - - - - - - - -gtaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaca