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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattccatattttatgcagtctaacttttttttcagttagagggaattgttccttttcaactggtcaactaatttcagttaaaatacgtgcttttcactatag

Basic information

species Glycine max
transcript GLYMA15G12100.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12100.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 5'ss of exon 12
ATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattccatattttatgcagtctaacttttttttcagttagagggaattgttccttttcaactggtcaactaatttcagttaaaatacgtgcttttcactatag-------------------------------------
|||||||||| |||| ||||||||||| |||||||||||||| ||||||||| | ||||||||||||||||| |||||||| ||  | ||||| |||||| ||||  |  || | |  ||    |  |  |  |    | |    |  | |   |||| ||     ||  ||  || | |     ||  || || |    |||                                      
ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCTgtatgatttaaatttgtttataggaagatgtcgtagtgctcttgttctacct-tctttttttaatgcagcacatagcttaaatagttgtaaatgtttcttgg-atatttttctgaagttcacctgccacattaatttcacacag

upper sequence: GLYMA15G12100.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv00s0187g00300.t01 (Vitis vinifera), 5'ss of exon 9
ATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattccatattttatgcagtctaacttttttttcagttagagggaattgttccttttcaactggtcaactaatttcagttaaaatacgtgcttttcactatag-------------------------------------
|||||||||| |||| ||||||||||| |||||||||||||| ||||||||| | ||||||||||||||||| |||||||| ||  | ||||| |||||| ||||  |  || | |  ||    |  |  |  |    | |    |  | |   |||| ||     ||  ||  || | |     ||  || || |    |||                                      
ATATTGGACACTGACTCAACAACTTGCACACCATACAATCAATGGTTGCAACTTAAGGCCAGGCGATCTCCTTGGAACTGGAACCATAAGTGGACCTgtatgatttaaatttgtttataggaagatgtcgtagtgctcttgttctacct-tcattttttaatgcagcacatagcttaaatagttgtaaatgtttcttgg-atatttttctgaagttcacctgccacattaatttcacacag
















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|207702269|gb|GD683024.1|GD683024
EST:     GGCCGGGCGATCTTTCCTTCGGTAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GGCCAGGCGATC--TCC-TCGG-AACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|22930747|gb|BU547886.1|BU547886
EST:     GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|207798026|gb|GD768114.1|GD768114
EST:     GGCCGGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|208334135|gb|GE132472.1|GE132472
EST:     GGCCGGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|208126686|gb|GD921142.1|GD921142
EST:     GGCCGGGCGATCTTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GGCCAGGCGATC-TCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|193300915|gb|FK267326.1|FK267326
EST:     CGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: CGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|193581906|gb|FK533191.1|FK533191
EST:     GGCCGGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|58015544|gb|CX702286.1|CX702286
EST:     GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|151402383|gb|EV272196.1|EV272196
EST:     GCAACCTTAGGCCAGGCGACCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|193698582|gb|FK638043.1|FK638043
EST:     GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
EST: gi|193352214|gb|FK317646.1|FK317646
EST:     TCGGAACTGGGACAGTTAGTGGTCCT                         GAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC
genomic: TCGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactatagGAGCCGGAGTCCCGGGCATGCTTGCTAGAATTAACGTGGAATGGACAAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTGGACATTGACCCAACAACTTGCTCACCATACAATCAACGGTTGCAACCTTAGGCCAGGCGATCTCCTCGGAACTGGGACAGTTAGTGGTCCTgtaagattccatattttatgcagtctaacttttttttcagttagagggaattgttccttttcaactggtcaactaatttcagttaaaatacgtgcttttcactatag

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