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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaccattttgctttcaaattttgtttttccacgctttagttttagttctcttcgtgattgtcaagaaggaaactttgtcttaactcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTA

Basic information

species Glycine max
transcript GLYMA15G02350.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02350.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g03410.t01 (Vitis vinifera), 3'ss of exon 4
tagaccattttgctttcaaattttgtttttccacgctttagttttagttctcttcgtgattgtcaagaaggaaac---tttgtctta--actcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTA
      | ||  | |    |||  | ||||| | || |  | |||| || | ||   || ||  || |    |     ||||||| |    |   ||   || |||||||||||||||||||||||||||| | || | |||||| |||||||||||| | ||||| || ||  | ||||| ||||| || ||||| ||||||||
---gttacttcacatc---attccgattttcaaagcatccggtttaattatgttttggaatgataacatctcattatgtttgtctcattgttttttgtgttttagCTCAAAGAGATTCCTCTGCTGGTGGAATCCAGACCAAGCATGAGGAAGAGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTA
















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|11413713|gb|BF425724.1|BF425724
EST:     CGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: CGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|193692550|gb|FK627669.1|FK627669
EST:     TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|208133124|gb|GD931729.1|GD931729
EST:     TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGG
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGG
EST: gi|298178211|gb|HO023946.1|HO023946
EST:     TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|192309095|gb|FG999056.1|FG999056
EST:     TG-AAATCTCTCTTCCGCCGCGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|298178855|gb|HO024590.1|HO024590
EST:     TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
EST: gi|19269416|gb|BM885672.1|BM885672
EST:     TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTG                         CTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA
genomic: TGAAAATCTCTCTTCCGCCGTGGACGAGCTATTCAGAGGTCTTCTTGCTGgtaatttttg ... tgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctcttcgtgattgtcaagaaggaaactttgtcttaactcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTA
                                      aactcac  putative branch site (score: 2)
                          aaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaccattttgctttcaaattttgtttttccacgctttagttttagttctcttcgtgattgtcaagaaggaaactttgtcttaactcactgctgttcagCTCAAAGAGATTCCTCTGCTGGTGGAGTTCACAACAAGCAGGAGGAAGAGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA