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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttattttatgatctctatcaaagtcctctgttttattagttattggcatatccatttgttcttaatctattttgtggacactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA

Basic information

species Glycine max
transcript GLYMA03G27460.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 3'ss of exon 14
gttttattttatgatctctatcaaagtcctctgttttat-tagttattggcatatccatttgttcttaatctattttgtggac------actttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA
    |||  |   || |    |  |  | |||| | ||  ||| || |  ||  | |  |  |    |||  | || | |  |      ||| |  ||||  ||||||||||||| |||||||||||||| |||||||| | |||||  ||  | | ||| ||||| || || |  || ||  ||||| | ||||  |
---gtatgctcaaatgttatcccta--catctgatatacatagatacttccactttccatgctcagaaattgacttggggagctctatgactctttagGCAATTGTAAGTGAGTACGCTGTGACTGGAAAGGATGCTGGCAAAGGAACACTGGTAGAAGCACTAGCAGAGGCAGCATTTCTCGTTGGATTAGAAAGAA

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 12
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 13
gttttattttatgatctctatcaaagtcctctgttttattagttattggcatatccatttgttcttaatctattttgtggacact--ttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA
   |    | ||    | || ||||   ||   ||  |  |   |   |   |  | ||     ||   ||   | ||| ||  |  |||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||  | ||  | || || ||||||| ||| || ||||| || |||||||
--gtgcggtaatagattataacaaaa--cttaattccaacaaacacaagatgaagctttcagcgttttactcactcgtgaactttgtttacagGCTTTTGTCAGTGAATATGCTGTTACTGGAAAAGATGCTGGTACAGGAAGCCTTCTTGCCTCTCTTGCAGAAGCTGCGTTTCTCATTGGTCTTGAAAAGA

upper sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 14
gttttattttatgatctctatcaaagtcctctgttttattagttattggcatatccatttgttcttaatctattttg----tggacactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA
           ||   |  |      || |||| || |  | |  | |   ||      || || | | || || ||    || |   ||| ||||||||||| ||||||||||||||||| || |||||||||||  ||||||  || ||||||||  | ||||||||||  ||||| |||||  |||||||||
----------gtgtggtgaaatgccttcatctgattcacaaatc-tagctctaaatgaatgctcctgaactgttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA

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|7796787|gb|AW782181.1|AW782181
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTNTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACANGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|6134767|gb|AW133160.1|AW133160
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|9819826|gb|BE555402.1|BE555402
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|19348102|gb|BM892634.1|BM892634
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|9899023|gb|BE607991.1|BE607991
EST:     CATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: CATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|9819476|gb|BE554989.1|BE554989
EST:     TGTTTTCTAGAGCTAATGCATNTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|6071989|gb|AW101436.1|AW101436
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGNGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|22523744|gb|BU082555.1|BU082555
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|51335508|gb|CO979374.1|CO979374
EST:     TGTTTTCTAGAGNNAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGN
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|21600500|gb|BQ610831.1|BQ610831
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
EST: gi|27424547|gb|CA936067.1|CA936067
EST:     TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAG                         GCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC
genomic: TGTTTTCTAGAGCTAATGCATTTGATCATACATCTCGAAATGGTCCAAAGgttttatttt ... cactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattagttattggcatatccatttgttcttaatctattttgtggacactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA
                          tcttaat  putative branch site (score: 3)
                         ttcttaatctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttattttatgatctctatcaaagtcctctgttttattagttattggcatatccatttgttcttaatctattttgtggacactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG