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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcctctctcaaaaccctaattaattccccttttttgtatttagttttggttatgcttgattttgtgtttatgggtttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG

Basic information

species Glycine max
transcript GLYMA06G23570.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G23570.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 2
gtactcctctctcaa-aaccctaattaattccccttt--tttgtatttagttt---tggttatgcttgatttt---gtgtttatgggtttctatt---agATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG
||  |    | | || ||   | ||   ||    | |  ||  ||||||| ||   | ||| |  ||  ||||    ||||||   |||| | |    |||||||||||||||||| |||  ||||||||| || ||||| ||||| || ||||| ||||| ||||  ||||| |||
gtgatttattgtaaacaaaattgatgggtttgtttataattgatatttagattacctagtttttttttttttttaaatgtttaattgtttttttccacagATATACAGAGAGAAGAGAAAGGTGTGCAGAAAGCAATTAGGGAAGCAGCCAAGAGAAATGATATGGTGTCTGCTAAG
















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|151393870|gb|EV263745.1|EV263745
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCAA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAA
EST: gi|192311177|gb|FK004488.1|FK004488
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAA-TGTGCAGAAGGCTATTAGAGAAGCTGCA
EST: gi|192311178|gb|FK004489.1|FK004489
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAA-TGTGCAGAAGGCTATTAGAGAAGCTGCA
EST: gi|42723184|gb|CK769083.1|CK769083
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCAA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAA
EST: gi|254334772|gb|GR844557.1|GR844557
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCAA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAA
EST: gi|151403536|gb|EV273346.1|EV273346
EST:     GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCG                         ATATACAGAGAGAAGNNNNNNNTGTGCAGAAGGCTATTAGAGAAGCTGCAA
genomic: GCAGCGCAGGCTTCGCCAAGAGTGTCGCAACATTGAGCGCCAAATTCGCGgtactcctct ... tttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtatttagttttggttatgcttgattttgtgtttatgggtttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG
                        gcttgat  putative branch site (score: 5)
                                             tttctatt  putative PPT
       tatttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcctctctcaaaaccctaattaattccccttttttgtatttagttttggttatgcttgattttgtgtttatgggtttctattagATATACAGAGAGAAGAAAAAAATGTGCAGAAGGCTATTAGAGAAGCTGCAAAGAGGAATGACATGGGCTCTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG