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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttggttagaactttttctgatattttttgttccttataatattgaataactgatattgtaagttgtatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA

Basic information

species Glycine max
transcript GLYMA19G22420.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
tcatttggttagaactttttctgatattttttgttccttataatattgaataactgatattgtaagttgtatttactt-----gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA
           | |  |||||  | | || |  | | |   | | || ||  |     ||   | | |||  || |||     |||| || ||||  ||   | ||||||||||||| ||||| ||||| ||| |||| | ||||||||| ||   ||||||||| |||||||||| ||||||||| ||  |    || |  || |
----caaaaatgtatattttcctacaattctcat-cttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA

upper sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
-tcatttggttagaactttttctgatattttttgttccttataatattgaa-taactgatattgtaagttgtatttactt-gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTC--CTAGAAGTGTACGAGAAA
  |    | |    |  |||||  | | || | || | | | | | || ||    |  ||| ||    || |  ||| |  |||| || ||||  ||   | ||||||||||||| ||| | ||||| ||| |||| | ||||||||| ||   ||||||||| |||||||||| | ||||||| |  |   |||||  |||||  
ggcgaaagatccata--ttttcctacaattctcgt-cttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA--

upper sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
--tcatttggttagaactttttctgat----attttttgttccttataatattgaataactgatattgtaagttgtatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA
  | |      || |  ||  |   ||     | ||    |   || |   |   |||| || | ||||   || | |   | |||| | || |    |   | ||||||||||||| ||| | ||||| ||| |||| | |||||| || ||   ||||||||| |||||||||| ||||||||| ||  |    || || || |
ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataa-tgctgttgttgcttat-taagcatgcactgttct----gatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA

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|192333795|gb|FK025840.1|FK025840
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAG-ATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|15000044|gb|BI320858.1|BI320858
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|192323120|gb|FK015246.1|FK015246
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|192316668|gb|FK008261.1|FK008261
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGA
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGA
EST: gi|10235787|gb|BE804675.1|BE804675
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|151411877|gb|EV281688.1|EV281688
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|15814202|gb|BI786477.1|BI786477
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|192316667|gb|FK008260.1|FK008260
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAAGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|192309334|gb|FK000542.1|FK000542
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|17022267|gb|BM093301.1|BM093301
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
EST: gi|192309335|gb|FK000543.1|FK000543
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTCCCTAGAAACAAACTACGTGATgtaagtgcta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaataactgatattgtaagttgtatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA
                                   attattgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttggttagaactttttctgatattttttgttccttataatattgaataactgatattgtaagttgtatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT