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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatctcaccatttactaccatgctctgcacacgtgtgcatgctgccatgtagaaaaagtttgtgaaacatttatggaaatgtcacttatttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTAAGATCTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGT

Basic information

species Glycine max
transcript GLYMA20G38960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 3
gaaatctcaccatttactaccatgctctgcacacgtgtgca--tgctgccatgtagaaaaagtttgtgaaacatttatggaaatgtcacttatttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTAAGATCTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGT
   || | |  | ||     | |  ||||    | ||      || |   | ||  || |||||  ||||   |   |    ||   |  | |||   |||||||||||||||| |||| || || ||||||||  ||||||| |||||||||||||||||| | |||  ||| ||||||||||| ||||| |||||| |||
--tattttattacttttatgctttttctgtgtgcttgaaagattgttatgaagtgaaataagttattgaactctcagtcacgatagtatctctttcaatcagGATAGAACTGCCTTGCTGTTTCTTCTTTTTCCATCAACACTACTTATTCTAAGATCTTGGATATGGGATGGTTGCTTGCCAACGTTTCCAGTTCAGCTGT
















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|14259702|gb|BG882610.1|BG882610
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|298182431|gb|HO026606.1|HO026606
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|14258798|gb|BG881706.1|BG881706
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|213590375|gb|DB963896.1|DB963896
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|298199045|gb|HO042408.1|HO042408
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|192319099|gb|FK010635.1|FK010635
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|192320395|gb|FK012253.1|FK012253
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|209701984|gb|BW664584.1|BW664584
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
EST: gi|213594582|gb|DB958001.1|DB958001
EST:     CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGG                         GATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA
genomic: CCAGGAAGGACGTTCAGCTCAAGGTCAAAGAGGAATACAACAGTTACAGGgtatatattt ... tttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatgtagaaaaagtttgtgaaacatttatggaaatgtcacttatttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTAAGATCTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGT
                                      tcacttatttttttc  CT-rich tract
                                      tcacttattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatctcaccatttactaccatgctctgcacacgtgtgcatgctgccatgtagaaaaagtttgtgaaacatttatggaaatgtcacttatttttttcagGATAGAACTGCCCTGCTATTCCTGCTTTTTCCGGCAACACTGCTTATTCTAAGATCTTGGGTTTGGTCTGGATGCTTGCCAACTTTTCCTGTTCAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - tcaccat
- - - - - - - - - - catgctc
- - - - - - - - - - - - - -tgcacac
- - - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcact