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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatattttaatgattgtgaatatagcattttatttttatttttttatttattttgaataatttaataacttccaaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG

Basic information

species Glycine max
transcript GLYMA08G09050.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------ttttatattttaatgattgtgaatatagcattttatttttatttttttattt------------attttgaataatttaataactt----ccaaaca-tttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
                                                  ||||  |||| |||   | || | |    |   |    | |||| || |               || ||| | | |||| |  |||    |  |||| | |  || |  |  || |||| |||||||||||||| ||||| ||||||||||||||||| || || || || |||||||||||||| || ||||||||| |||
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG

upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
ttttatattttaatgattgtgaat-atagcattttatttttatttttttatt-tattttgaataatttaataacttccaaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
  ||   |||  |   || |   | ||    ||   |  | ||  | || || ||  ||||||  || | |        ||   |   ||   |||||| |||| |||||||||||||| || || || |||||||| || || ||||| |||||||| || || ||||| ||||||||||||||||
--ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
















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|58024174|gb|CX710915.1|CX710915
EST:     TATCACCATGGAAGGGTAT-CTTCTTTTTGGCCCACCGGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|58023441|gb|CX710182.1|CX710182
EST:     GGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAAC-TTTTTTAAT
genomic: GGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|58024561|gb|CX711302.1|CX711302
EST:     TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|58018662|gb|CX705404.1|CX705404
EST:     TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|10848344|gb|BF071723.1|BF071723
EST:     TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: TATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|58020971|gb|CX707713.1|CX707713
EST:     GGCCCACCGGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: GGCCCACCGGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT
EST: gi|58021561|gb|CX708302.1|CX708302
EST:     GGGGACAGGAAAG                         ACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACNNNNNNNAAT
genomic: GGGGACAGGAAAGgtttgtattg ... attgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttattttgaataatttaataacttccaaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
     ttattttgaataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttatattttaatgattgtgaatatagcattttatttttatttttttatttattttgaataatttaataacttccaaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG

- - - - - - - gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg