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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattagtagacctaggagaaattctgtacagacgggagagtatgtaaaagcttcattcttctccatgttctaacaatgatgattacttaacattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG

Basic information

species Glycine max
transcript GLYMA08G18760.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------------------acattagtagacctaggagaaattctgtacagacgggagagtat---gtaaa------agcttcattcttctccatgttctaacaatgatgattacttaa-------cattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG
                                                                              ||  |  |     | || |   |||| | |  ||  ||   ||    | | |       | ||||    ||||  | || |      |||  |||   ||         |   |||| |||||| || || |||||||||||||| |||||||||||||| |||||  | ||||||||||| ||||| || |||
gtctgtattatttaaaattaaaaattctatgtgttcctgtacttctcgtcaaaccactcctgtattcattttctcctgaccctgctcttttttgggggt-ttctttgcttacatgaatttacagggcagatcttttggattcacatgtctcagtatttttttgtggatttttatacaagttattttttcttcagGTTGCTGAACAGGAATATGAGAAAGAAAAACTGAATGAGAGAATAGCTAAGCTCTCTGGTGGTGTTGCTGTCATCCAG

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 8
-----acattagtagacctaggagaaattctgtacagacgggagagtatgtaaaagcttcattcttctccatgttctaacaatgatgattacttaacattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG
      ||||       || | |    | |   |   ||    || |  |  |||  | | ||||  |  ||| | ||      |  |  | | || |||  |||||| |||| ||||| ||||||| |||||| || || ||||| || |||||| | ||||||||||| ||||| || |||
agcctgcattcccctgtcttgcatgtctccacaagccacttctgatttggataaaaatgctttctagta-atggt-tagttccaa--aacattcaa-attttcagGCTACTGAACAAGAATATGAGAGAGAAAAACTAAACGAGAGGATAGCTAAACTCTCTGGTGGTGTTGCTGTCATTCAG

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 8
acattagtagacctaggagaaattctgtacagacgggagagtatgtaaaagcttcattcttctccatgt-tctaacaatgatgattacttaacattaac--agGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG
                          |||||      | |  ||  ||| |   || |    |   | | | | ||  |||| |   |||    ||     |||||||||| ||||| ||||| || |||||||| |||||||||||||||||||| || || ||||| ||||| || |||
--------------------------gtacatctcaaaaaacattgaaatgtcccaataaattggttttatgttacggtgattaagtctttgggtttgtgtagGCTGCTGAACAAGACTATGAAAAGGAAAAGCTTAATGAGAGAATTGCTAAATTATCAGGCGGTGTTGCTGTAATTCAG

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|193539742|gb|FK495212.1|FK495212
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193622348|gb|FK568170.1|FK568170
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|151412595|gb|EV282407.1|EV282407
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193397248|gb|FK362876.1|FK362876
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16284130|gb|BI945921.1|BI945921
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16281997|gb|BI944781.1|BI944781
EST:     CCCAGGAAGCAGCGAACAACAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTCTGACAAACAAAAGCTGAATGAGACAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|298191386|gb|HO038865.1|HO038865
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16284918|gb|BI946338.1|BI946338
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|20449400|gb|BQ253524.1|BQ253524
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|151401848|gb|EV271661.1|EV271661
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|20075657|gb|BQ094440.1|BQ094440
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16282846|gb|BI945236.1|BI945236
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16279729|gb|BI943586.1|BI943586
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208046607|gb|GD844319.1|GD844319
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208217316|gb|GE010350.1|GE010350
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|15813847|gb|BI786122.1|BI786122
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|17964146|gb|BM270885.1|BM270885
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16276796|gb|BI942048.1|BI942048
EST:     CCANGAAGCAGTGAACAAGAGAAGGTGCCCAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCAGGAAGCAGTGAACAAGAGA-GTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|207710160|gb|GD691208.1|GD691208
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16279198|gb|BI943310.1|BI943310
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16278942|gb|BI943174.1|BI943174
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACANATTAGGAACCTAATTGAG                         GCTGCTGAACAAGAGTAT
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTAT
EST: gi|27426513|gb|CA938033.1|CA938033
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16344875|gb|BI970470.1|BI970470
EST:     AACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGANNNGCTGAATGAGAGANNNGCTAAA
genomic: AACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|298172173|gb|HO021765.1|HO021765
EST:     CCCAGGAAGCAGTGAACAAGGGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCCAGGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAG-AGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAA
EST: gi|298196897|gb|HO041640.1|HO041640
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16284535|gb|BI946141.1|BI946141
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16276810|gb|BI942056.1|BI942056
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16278862|gb|BI943133.1|BI943133
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|7925872|gb|AW831898.1|AW831898
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTANA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgttgttcctt ... acattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTA-A


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagcttcattcttctccatgttctaacaatgatgattacttaacattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG
                                     attacttaacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acattagtagacctaggagaaattctgtacagacgggagagtatgtaaaagcttcattcttctccatgttctaacaatgatgattacttaacattaacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAATTGTCTGGTGGTGTGGCTGTGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG