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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattccattgaactcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG

Basic information

species Glycine max
transcript GLYMA11G07530.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07530.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
aaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattccattga-actcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG
   | | |   | |||    || ||   |  |   || |     ||| |  |    | ||    ||||||   |    ||     | || |||  || ||||| ||||||||| |||||||  | ||||||||||| ||||| |||||||  ||||| ||||| |||
--gtaagtttta-tcttcttctacattgcggaagattagatcatattaagaaagttagtgctggtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG

upper sequence: GLYMA11G07530.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 2
---------aaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattcca--ttgaactcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG
         |  |||  ||  || |     ||   |  | | | | ||  | |  |||  | |  |  | | | || |  ||||    |  |||      ||    ||||||| |||||||||||||| || || ||||||||||||||||| |||||  |||||||  | ||||||
taggaggccatgtcataagttgttt-----ttagtagatgaaagtatgtttcctctgacaaatttaggtggcattcctaattcttaacatgtaa------tttttgggcagGTAGTTGAAATTGGCAAGGGCAGCAAGGTTAAGTATGAGCTTGACAAAGCAAGTGGCTTGATAAAG
















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|33390382|gb|CA853577.1|CA853577
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|10235681|gb|BE804569.1|BE804569
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|58018488|gb|CX705230.1|CX705230
EST:     GGAGCTCCAGCAGTTTTCAACTGT                         GTGG-TGAAATTGGCCAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|151395789|gb|EV265666.1|EV265666
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|58014268|gb|CX701010.1|CX701010
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192310085|gb|FK000649.1|FK000649
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192316515|gb|FK009312.1|FK009312
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192331258|gb|FK023769.1|FK023769
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192321263|gb|FK014353.1|FK014353
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|58022382|gb|CX709123.1|CX709123
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|58017496|gb|CX704238.1|CX704238
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|151402592|gb|EV272405.1|EV272405
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|15661703|gb|BI699074.1|BI699074
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|7686402|gb|AW757050.1|AW757050
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|209729103|gb|BW655080.1|BW655080
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|37996150|gb|CF807739.1|CF807739
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCGTGGACAAGAC
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGC-TGGACAAGAC
EST: gi|192333273|gb|FK026154.1|FK026154
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|15203687|gb|BI426455.1|BI426455
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|11273956|gb|BF324342.1|BF324342
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|21595665|gb|BQ610566.1|BQ610566
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGATATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|213596795|gb|DB964086.1|DB964086
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|26057763|gb|CA800677.1|CA800677
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|19452855|gb|BM954265.1|BM954265
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|58017619|gb|CX704361.1|CX704361
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|12689521|gb|BG155857.1|BG155857
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|151406239|gb|EV276054.1|EV276054
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|254336463|gb|GR842642.1|GR842642
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|17022265|gb|BM093299.1|BM093299
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|15814337|gb|BI786612.1|BI786612
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|6481455|gb|AW200726.1|AW200726
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192321262|gb|FK014352.1|FK014352
EST:     GATTGGGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GATTGGGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192316544|gb|FK009313.1|FK009313
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|9986810|gb|BE660918.1|BE660918
EST:     GGCCAGGAGCTCCAGCTGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGCAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|192294924|gb|FG986647.1|FG986647
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
EST: gi|209711074|gb|BW676430.1|BW676430
EST:     GGCCAGGAGCTCCAGCAGTTTTCAACTGT                         GTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA
genomic: GGCCAGGAGCTCCAGCAGTTTTCAACTGTgtaagctttt ... tcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattattccattgaactcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG
 cattgat  putative branch site (score: 4)
                                aaataaatcgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattccattgaactcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - cactagc
- - - - - - gtctgaa
- - - - - - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa