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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcggcgtaggtttaaaaaataaaaattgaaggaaaaatagaatgattgaatttggattttgagtgatggacggagttgacgattcttctggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAGAAGCAAGCGAGGCTCGCCGGCGACGTCGCCGCCACCAGAAACGCCGTCA

Basic information

species Glycine max
transcript GLYMA04G39520.1
intron # 1
splice site 3'
intron type U2

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|20812745|gb|BQ297231.1|BQ297231
EST:     CTTCCCTGGTTATGGCTATG                         GAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
genomic: CTTCCCTGGTTATGGCTATGgtacgccccc ... ggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
EST: gi|20207825|gb|BQ133914.1|BQ133914
EST:     CTCCCCTCCTGCACGCAAAGTAGCAAACTTCCCTGGTTATGGCTATG                         GAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
genomic: CTCCCCTCCTGCACGCAAAGTAGCAAACTTCCCTGGTTATGGCTATGgtacgccccc ... ggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
EST: gi|193483670|gb|FK452801.1|FK452801
EST:     GCAAACTTCCCTGGTTATGGCTATG                         GAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
genomic: GCAAACTTCCCTGGTTATGGCTATGgtacgccccc ... ggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
EST: gi|15284713|gb|BI468604.1|BI468604
EST:     GTAGCAAACTTCCCTGGTTATGGCTATG                         GAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
genomic: GTAGCAAACTTCCCTGGTTATGGCTATGgtacgccccc ... ggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
EST: gi|192297411|gb|FG990689.1|FG990689
EST:     CTTCTCCCCTCCTGCACGCAAAGTAGCAAACTTCCCTGGTTATGGCTATG                         GAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG
genomic: CTTCTCCCCTCCTGCACGCAAAGTAGCAAACTTCCCTGGTTATGGCTATGgtacgccccc ... ggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaatttggattttgagtgatggacggagttgacgattcttctggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAGAAGCAAGCGAGGCTCGCCGGCGACGTCGCCGCCACCAGAAACGCCGTCA
                             agttgac  putative branch site (score: 4)
                                      ttcttctg  putative PPT
           attttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcggcgtaggtttaaaaaataaaaattgaaggaaaaatagaatgattgaatttggattttgagtgatggacggagttgacgattcttctggattttcagGAGAACGCCGGGAATTTAGAAGCGGCCATAGAACAATTGCTGAATGCGGAGAAGCAAGCGAGGCTCGCCGGCGACGTCGCCGCCACCAGAAACGCCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - aaaaaat
- - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg