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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacatcctgcgtcattataactataaacccaaaaatagaattaactctgaatgcatgtgtgtgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAAGTGCGGCGCTTGCGCATCCAGAGACGTGCATGGAGGGATTCGAAGGGAC

Basic information

species Glycine max
transcript GLYMA17G04940.1
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|5342503|gb|AI794787.1|AI794787
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGACTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|6134357|gb|AW132750.1|AW132750
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|6455806|gb|AW186489.1|AW186489
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|9986454|gb|BE660562.1|BE660562
EST:     CCCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|213602887|gb|DB972461.1|DB972461
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|9986453|gb|BE660561.1|BE660561
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|20811818|gb|BQ296296.1|BQ296296
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|9986455|gb|BE660563.1|BE660563
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|213616694|gb|DB969190.1|DB969190
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|23726353|gb|BU761167.1|BU761167
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|9986456|gb|BE660564.1|BE660564
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|17021842|gb|BM092876.1|BM092876
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|24136118|gb|BU926628.1|BU926628
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|213589918|gb|DB959473.1|DB959473
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAA
EST: gi|9264580|gb|BE352727.1|BE352727
EST:     CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAG                         GGAAGCATAACAAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTA
genomic: CTCCTCCGACGTCCTCTCCTGGGCCCTCTCGGCCTCTCAGAACCCCAAAGgtacacatcc ... tgtgtggcagGGAAGCATAACA-GTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactataaacccaaaaatagaattaactctgaatgcatgtgtgtgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAAGTGCGGCGCTTGCGCATCCAGAGACGTGCATGGAGGGATTCGAAGGGAC
                      aattaac  putative branch site (score: 2)
              aaaaatagaattaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatcctgcgtcattataactataaacccaaaaatagaattaactctgaatgcatgtgtgtgtgtggcagGGAAGCATAACAGTACGGGGAACCTGAGTTCGGATTTGAGGACATGGCTAAGTGCGGCGCTTGCGCATCCAGAGACGTGCATGGAGGGATTCGAAGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG