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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag

Basic information

species Glycine max
transcript GLYMA08G18760.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 10
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttg-actttcag------------------------------------------------------------------------
|| || ||||| || || || ||||||||||||||||||||||| ||||| || || || ||||||||||||||      | | |        | |     | |    | ||  | ||  | |  ||      || || ||  | ||                                                                        
GTAGGAGCACAGACAGAAACTGAGCTCAAGGAAAAGAAATTGAGGGTTGAGGATGCCCTGAATGCTACAAAGgtaaatgctacatatggtggttctcacagtatacctgtatgttctcattcacatagcgtcctgatgcacaattagcactgtgatgatcttaaaatcctatttatttgtgatgagtccttgttagttgatagttttctatatttgcag

upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttcttt---cccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttga--ctttcag----
||||| |||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||  | |  ||| |   |  | ||  || | || |||      ||  | ||  ||  | ||  ||||||   |||| |     
GTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAGgtaacatcatctctaagcaaagagccttgaaatgtttcca---tccatatggtagagactaagttgttggaccttttaattag

upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttccca-----aagtttttagattttttgggattc-----tgtctgtaagctaatagtttgttgactttcag
||||| || |||||||||||||||||||| ||||||||  ||||||| ||||| |||||||||||||||||||||   || | | |||         | || ||| | |  ||  | ||     | |||  |   ||  |  |  |||| ||||||
GTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAGgtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcag

upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag--------
||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| |||||||||   || | ||||  |   ||   |    | ||       |    || | |||  | |     |  ||| |         
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag

upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag---------------------------------------
||||| |||||||||||||||||||| || ||||||||| ||||||| ||||||||||| ||||| || |||||     ||||||||   || || |   | |   | |     || ||   |   || |||      ||   |||                                       
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaa---tttctttcatgaaattatggcactgaattgctagttg-ctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag

upper sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag
||||| ||||||||||||||||| || || |||||||| || ||||| ||||| ||| | ||||| || |||||               |||    |  |||| |     ||| ||  ||||||    ||  |||  |        
GTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGgt---------------aaatagatcggattctggaatattgtgg-tgtaagtgtttaaattgcag--------

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|16282149|gb|BI944863.1|BI944863
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|151412595|gb|EV282407.1|EV282407
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16284130|gb|BI945921.1|BI945921
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16278312|gb|BI942837.1|BI942837
EST:     GCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: GCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|298191386|gb|HO038865.1|HO038865
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16278884|gb|BI943144.1|BI943144
EST:     GAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: GAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16284918|gb|BI946338.1|BI946338
EST:     AGCTCAAGGAGAAGAAATCGAGAGTTGAAGACGCTCTTAGTGCTACAAAG                         GCAGCTGTGGAAGAAGGTAT
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTAT
EST: gi|20449400|gb|BQ253524.1|BQ253524
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|151401848|gb|EV271661.1|EV271661
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16282846|gb|BI945236.1|BI945236
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16279729|gb|BI943586.1|BI943586
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|17964146|gb|BM270885.1|BM270885
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16284557|gb|BI946152.1|BI946152
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|193327142|gb|FK292407.1|FK292407
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTAATTGTTGTTGGTGGTGGTTGCACTCTTCTGAG
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTA-TTGTTGTTGGTGGTGGTTGCACTCTTCTGAG
EST: gi|193384610|gb|FK350168.1|FK350168
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTAATTGTTGTTGGTGGTGGTTGCACTCTTCTGAG
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTA-TTGTTGTTGGTGGTGGTTGCACTCTTCTGAG
EST: gi|16279198|gb|BI943310.1|BI943310
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGACGAAGGTATTGTTGGTGGGTG-TG-TTGCACTC
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGG-TGGTGGTTGCACTC
EST: gi|254322415|gb|GR837829.1|GR837829
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|27426513|gb|CA938033.1|CA938033
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAAGTATTGTTGTT
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTT
EST: gi|16344875|gb|BI970470.1|BI970470
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|208281737|gb|GE077693.1|GE077693
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|298172173|gb|HO021765.1|HO021765
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16281476|gb|BI944507.1|BI944507
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGA-GAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|298196897|gb|HO041640.1|HO041640
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16284535|gb|BI946141.1|BI946141
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAANGGTAT-GTTGT
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAA-GGTATTGTTGT
EST: gi|16276810|gb|BI942056.1|BI942056
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGGTGGACCTTTTTCTTG
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCAC-TCTT-CT-G
EST: gi|16278862|gb|BI943133.1|BI943133
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTCAATGCTACAAAG                         GCAGCTGTAGAGGAAAGTAT
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTAT
EST: gi|151401056|gb|EV270870.1|EV270870
EST:     AAGACGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AAGACGCTCTTAATGCTACAAAGgtgtcctttt ... tgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag

- - - - - - - - - - - AGCTCA
- - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA