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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttctgggcacctttttctctgtattccatttaccaaggacatttgacaactataaaatttgttttaaaaattgaattaataaagattttgttctttaacaatctctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAGGATGATGTTGAAGATGAAATAGCAGAAATCAAGGCAGCTCATTTTGAGG

Basic information

species Glycine max
transcript GLYMA19G36740.1
intron # 8
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|208041472|gb|GD838652.1|GD838652
EST:     AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAAAGAGATAACC
genomic: AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACC
EST: gi|298167324|gb|HO010763.1|HO010763
EST:     AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
genomic: AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
EST: gi|58021701|gb|CX708442.1|CX708442
EST:     GAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
genomic: GAGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
EST: gi|207769729|gb|GD741301.1|GD741301
EST:     AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAA-GAGATAACCCTG
genomic: AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTG
EST: gi|207717640|gb|GD697742.1|GD697742
EST:     AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
genomic: AGATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
EST: gi|208192302|gb|GD993678.1|GD993678
EST:     GATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAGAAGAACATTGAGAAG                         GACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG
genomic: GATTTGCCAGCGCGCGTGCAAGTATGCCATTAGAG-AGAACATTGAGAAGgtactgttct ... ctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttaaaaattgaattaataaagattttgttctttaacaatctctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAGGATGATGTTGAAGATGAAATAGCAGAAATCAAGGCAGCTCATTTTGAGG
                                 ctttaac  putative branch site (score: 3)
                                          tctctctt  putative PPT
     taaaaattgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttctgggcacctttttctctgtattccatttaccaaggacatttgacaactataaaatttgttttaaaaattgaattaataaagattttgttctttaacaatctctcttggcagGACATTGAGAGAGAAAGGAGGAAAAGAGATAACCCTGAAGCAATGGAAGAGGATGATGTTGAAGATGAAATAGCAGAAATCAAGGCAGCTCATTTTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA