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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacag

Basic information

species Glycine max
transcript GLYMA05G36620.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacag
||||||||||| |||||||||||||||||    ||||||||||| ||||| || |||| |||||| ||||| || |||||||| || |||||||| || ||| | |    |       |   |    || | |   |  ||  || | |     |  |  || |  || | | | ||    | | |  ||                    
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCATACCTTGGCAAGAAGATCAATGATGCTGTCGTCACTGTTCCTGgttagtaactgaacaattctgctggttacctctagtagttgttatgtaaaaacgtggcggct-cacttccttgtgttgtgtttttttgcag-------------------

upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttc-aactgcaatttgattgttttcctcctgcttttgcctttat-ttcaatatctcacattttcctttaaaatgcacag
||||||||||| |||||||||||||||||    ||||||||||| ||||| || || | |||||| ||||| || || ||||| || ||||||||||| ||| | |      ||| | || |   |   |||  || |   |   ||   |     |      ||||    | |||| ||   | | |  ||                    
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaa----ctgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag-------------------

upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttat-ttcaatatctcacattttcctttaaaatgcacag
|| |||||||| || ||||| ||||||||||||||||||||||| || || ||||| | ||||||||||||||| || || || || |||||||| |||||| |      || ||     ||  | |   |  |  |   | |  || ||| | |   |   |   |||  | | | ||   | | |   | ||| | |            
AGTCCTGAGGAGATTAGTGCTATGATTCTGACTAAGATGAAGGAGACAGCTGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgtta------gtttgttgttatatatg---tggtggagaggtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactttgcgtag----------

upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcct-cctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacag
|| |||||||| |||||||||||||||||||||||||||||||| || || ||||| | ||||||||||||||| || || || || |||||||| |||||| | |       |    |   |      |||| |     |      |||   |||| |  |||  || |   ||  ||   ||| |    |||  ||     |||| |||
AGTCCTGAGGAGATCAGTGCCATGATTCTGACTAAGATGAAGGAGACAGCCGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgact-----atgcgcag

upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgactta---tttcaactgcaatttgattgttttcct----cctgcttttgcctttatttcaatat---------ctcacatt---ttcctttaaaatgcacag
||||||||||| |||||||| |||||| |||||||||||||||| || || |||||||||||||| ||||| || || ||||| || || ||||| || ||| | |   | |||   | |  | |||  | |   ||| ||||||    | |   | ||| |      ||  || || |||  |||| ||          |||| |||   || |  |  ||  | |||
AGCCCTGAGGAGATCAGTGCAATGATTTTGACTAAGATGAAGGAGACAGCTGAAGCATTCCTTGGGAAGAAGATCAAGGATGCTGTCGTTACTGTGCCCGgtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatattagctttccatgcaacccgcag

upper sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 3
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacag
|| |||||||| || ||||| |||||||| || ||||||||||| || |||||||| ||||||||||||| ||| || ||||| || || || || || ||||| || ||  | |    | || | |  | |  | || |||        |||||| ||  ||   |  | | | |||| || ||| |||  |||               
AGTCCTGAGGAGATAAGTGCTATGATTCTAACAAAGATGAAGGAGACAGCGGAAGCTTTCCTTGGAAAGACAATCAAGGATGCAGTTGTTACAGTTCCTGgtaa-tgtaaaacagtttgatttgatggatgaagtaaattgc--------tgtttttctgttgagatgacttatgtttctat-tcttacaacttctacag----------

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|193665404|gb|FK613394.1|FK613394
EST:     GAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCA-GGATGCTGGTGTCATTG
genomic: GAAGCATTCCTTGGAAAGAAAATTAATGATGCCGT-GGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|9986537|gb|BE660645.1|BE660645
EST:     GAAGCATTCCTTGGGAAGAAAATTAATGATGCCCGTGGTCACTGTCCCA-                         CTTACTTCAATGATGCTCAAAGGCAG-CC-CCAAGGATGCTGGTGTCAT
genomic: GAAGCATTCCTTGGAAAGAAAATTAATGATGCC-GTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCAT
EST: gi|9987179|gb|BE661287.1|BE661287
EST:     GGAAGCATTCCTTGGGAAGAAAATTAATGATGCCGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
EST: gi|193548019|gb|FK505188.1|FK505188
EST:     GGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGNTGCTGGTGTCATTG
genomic: GGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaa ... aaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA