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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCTATGCTGATATGGTAAAGGCTGGAATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattatatcatcgcattcactacactgagtttatttatgaagtgcacaagtatgtgtaatttcagtgggttaaaatcatgttgtatcttaaattaaatcaagggtgaatacaagtcttgtgcattttaaagacaaacagtctttggctattattattgatttaactattttgttgtcatgcag

Basic information

species Glycine max
transcript GLYMA07G01190.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01190.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv09s0002g02240.t01 (Vitis vinifera), 5'ss of exon 16
GTGTCTATGCTGATATGGTAAAGGCTGGAATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattatatcatcgcattcactacactgagtttatttatgaagtgcacaagtatgtgtaatttcagtgggttaaaatcatgttgtatcttaaattaaatcaagggtgaatacaagtcttgtgcattttaaagacaaacagtctttggctattattattgatttaactattttgttgtcatgcag
|||| |||| ||||||||| || |||||||| ||||||||||||||||| || |||||||| |||||||||||||||||||||| ||       |  | ||| |        | ||||   ||| || ||  | |    || ||| | || |    || ||  || | | | || ||||| ||    |     | || | |                                                                 
GTGTGTATGTTGATATGGTTAAAGCTGGAATTATAGATCCTCTCAAAGTGGTCAGAACTGCCTTGGTAGATGCTGCCAGgtaaagtt-------cataatcagt--------tatattagagaaatgtacttgcaaa-atatttttactgagc---aacca-attttctttaaagttaaagca----ttggcccgagacctcc---------------------------------------------------------------
















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|51338205|gb|CO982071.1|CO982071
EST:     ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAG                         TGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
genomic: ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattat ... tgtcatgcagTGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
EST: gi|18040485|gb|BM308779.1|BM308779
EST:     ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAG                         TGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
genomic: ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattat ... tgtcatgcagTGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
EST: gi|22525526|gb|BU084337.1|BU084337
EST:     ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAG                         TGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
genomic: ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattat ... tgtcatgcagTGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
EST: gi|18714477|gb|BM522781.1|BM522781
EST:     TCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAG                         TGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
genomic: TCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattat ... tgtcatgcagTGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
EST: gi|298171846|gb|HO021438.1|HO021438
EST:     ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAG                         TGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA
genomic: ATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattat ... tgtcatgcagTGTGTCATTGCTACTGACAACAACCGAGGCAGCTGTGGTGGATAATTCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTCTATGCTGATATGGTAAAGGCTGGAATAATAGATCCTCTCAAAGTTGTTAGAACTGCTTTGGTAGATGCTGCCAGgtaaaattatatcatcgcattcactacactgagtttatttatgaagtgcacaagtatgtgtaatttcagtgggttaaaatcatgttgtatcttaaattaaatcaagggtgaatacaagtcttgtgcattttaaagacaaacagtctttggctattattattgatttaactattttgttgtcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC