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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTAAGCGTTGATGATTCTCTTGTATGTTCCTTTGAGATATTGAAACCCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatcaacaatcagctgttgtatttttttagagtcttgtattattttcgaacgtttgtgcatatcagtatcttatgcaactttttccgcag

Basic information

species Glycine max
transcript GLYMA03G39440.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39440.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G27840.2 (Arabidopsis thaliana), 5'ss of exon 3
---------------ATTGTTAAGCGTTGATGATTCTCTTGTATGTTCCTTTGAGATATTGAAACCCGCTGATAGAGCTTCAGGAAGTGGTTCA-TCAAAAATGAATTTTAAGAAGgtaaatatcaacaatcagctgttgtatttttttagagtcttgtattattttcgaacgtttgtgcatatcagtatcttatgcaactttttccgcag
                || ||||||||||| || |||||||||||||||||||||||  ||||||| ||      ||||||| | |||  | |  |||| || |    ||   |    | ||||  | | | |       | || |   | | |  |    ||    | |||     || |  |    | ||| || ||    ||      
TGACAACGCTGGTGCGTTATTAAGCGTTGACGAGTCTCTTGTATGTTCCTTTGAGATTATGAAACCAGCCCC---AGCTTCAAGCAGTCATCCTCTCAAGAAGgttagtttctaccaaagatatatagatttaagc-ccatcttataacacaattcttctgtaagaacaaac-----tgaaacttgaaaccttctgaaaaaccttatag--
















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|31305522|gb|CD390725.1|CD390725
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|207772354|gb|GD742639.1|GD742639
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|16344847|gb|BI970442.1|BI970442
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|6951976|gb|AW424044.1|AW424044
EST:     CAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|209698501|gb|BW656414.1|BW656414
EST:     TAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: TAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|31457076|gb|CD399104.1|CD399104
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|207797515|gb|GD769913.1|GD769913
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAG
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAG
EST: gi|19269934|gb|BM886190.1|BM886190
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCA
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCA
EST: gi|9985002|gb|BE659110.1|BE659110
EST:     CAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|7925834|gb|AW831860.1|AW831860
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|4260398|gb|AI416894.1|AI416894
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|13791695|gb|BG654286.1|BG654286
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
EST: gi|208129382|gb|GD930978.1|GD930978
EST:     CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAG                         CCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT
genomic: CCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatca ... ttttccgcagCCACCCAAACTTGGAAAGATATAGTATTTGGCAAGGATTTTCGGTTCAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTAAGCGTTGATGATTCTCTTGTATGTTCCTTTGAGATATTGAAACCCGCTGATAGAGCTTCAGGAAGTGGTTCATCAAAAATGAATTTTAAGAAGgtaaatatcaacaatcagctgttgtatttttttagagtcttgtattattttcgaacgtttgtgcatatcagtatcttatgcaactttttccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG