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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttttacttgtgttcaaatatggcaagagattgactagttgttccaattagaacagtgatgggtcacacgaaaatgatcattctatggatttatttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGCATGAAGAACCAAATGCAG

Basic information

species Glycine max
transcript GLYMA20G31630.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgttttactt--gtgttcaaatatggcaa------gagattgactagttgttccaatta-gaacagtgatgggtca--------cacgaaaatgatcattctatggattta-------tttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGCATGAAGAACCAAATGCAG
|| ||| ||| |  |  |  ||  ||  |  | |       | ||| |    |||   ||  || | |  | |  ||   |        || || ||  || ||| | | |||||        ||| || |||||||||| ||||| ||||||||||| || || || ||||| || || ||||||||||| ||||||||||||| ||| ||||||
gtaagtatttaaactcagaatttgaacctctccactctgcaaaattcatagcttggggcagatatggaatgagggggactaaattgtatcaggataaacataattatgttgatttgcatgttttttctgcagGGAGCAATCATGGCGGTTGGAGCATCAGAACCAACCGTTGTTGCCACCAAGGATGGTCGGATTGGCATGAAGAGCCAGATGCAG
















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|208326317|gb|GE121483.1|GE121483
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|207842036|gb|GD813696.1|GD813696
EST:     CGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: CGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|208164905|gb|GD962879.1|GD962879
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACTTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|192313139|gb|FK003721.1|FK003721
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|18039518|gb|BM307812.1|BM307812
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|208310067|gb|GE109795.1|GE109795
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|7691381|gb|AW759439.1|AW759439
EST:     TGGGAATGTATGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGCAACT                         GGAGCAATAATGGCTGTT
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTT
EST: gi|208249676|gb|GE045439.1|GE045439
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTG
EST: gi|193609301|gb|FK562949.1|FK562949
EST:     TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|208143451|gb|GD942469.1|GD942469
EST:     CCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: CCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|298180893|gb|HO022332.1|HO022332
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|192313138|gb|FK003720.1|FK003720
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|193555157|gb|FK515154.1|FK515154
EST:     TGGGGATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|208274109|gb|GE073285.1|GE073285
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACTTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|22929725|gb|BU546864.1|BU546864
EST:     TGGGAATGTNNNGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|7591481|gb|AW707213.1|AW707213
EST:     TGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|207681905|gb|GD662470.1|GD662470
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|193545458|gb|FK503531.1|FK503531
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|207721332|gb|GD702389.1|GD702389
EST:     T-GGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|193664881|gb|FK611625.1|FK611625
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|9204994|gb|BE331218.1|BE331218
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|207753601|gb|GD725999.1|GD725999
EST:     TGGGAATGTTTGACGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
EST: gi|207823490|gb|GD794109.1|GD794109
EST:     TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT                         GGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG
genomic: TGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagtgttt ... atttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaacagtgatgggtcacacgaaaatgatcattctatggatttatttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGCATGAAGAACCAAATGCAG
                                          tttattt  CT-rich tract
                                         atttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttttacttgtgttcaaatatggcaagagattgactagttgttccaattagaacagtgatgggtcacacgaaaatgatcattctatggatttatttgtgtagGGAGCAATAATGGCTGTTGGAGCATCCGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGCATGAAGAACCAAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC