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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaattagttttggtattgataatgagatggaataggagcaaagttgttgggcatgattcccatcttatagcactgattctttttctctcttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA

Basic information

species Glycine max
transcript GLYMA03G22220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22220.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------agaattagttt-tggtattgataatgagatggaataggagcaaagttgttgggcatgattcccatcttatagcactgattct-----------------ttttctctcttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA
                       ||| | | | | |  ||   || ||||  || |  |       |||| ||     | | | | |  |||  | |   ||  |                 || | | |  |   | ||| || ||||| |||||  |||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||||||
gtaagtataattgtgtttcatagagattcattgtatattagccatcatgaattgaagaatttagtcagtt-ttatatgttacttctaggttagtgaatcaatgttgaatattgttgaagaagttatgtttgctccttgcagAGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGA

upper sequence: GLYMA03G22220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g01400.t01 (Vitis vinifera), 3'ss of exon 3
agaattagttttggtattgataatgagatggaataggagcaaag--ttgttgggcatgattcccatct-tatagcactgat-tctttttctctcttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA----------------------
    ||||  |  | |  ||    |||   | | |    |||||  ||||  ||  | |   |  | | | |  | || |  |||   |||||      ||||| |||||||||||||| || |||||||||||||| |||||||| ||||| |||||||||||||||||||||||||||||                      
---gttagcatgagaaa-gagggagagtctgtacattcacaaagagttgtctggttttaaatcagtgtctctctcgctaacctctgcctctcttcccacttcagAGTATTTGAAAAGTCCCTACAGTATGTGAAGCGCTTCAGCCGGTATAAGAATCCTGATGCTGTTAGACAAGTTCGAGAAATTCTGAGCCGATACCAGTTG
















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|254340129|gb|GR858254.1|GR858254
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|6964421|gb|AW433114.1|AW433114
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|192308232|gb|FK001302.1|FK001302
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|193512606|gb|FK471806.1|FK471806
EST:     GCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: GCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|192308233|gb|FK001303.1|FK001303
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|208159032|gb|GD951757.1|GD951757
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGA-GCGTTTCAGCCG
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCG
EST: gi|298185814|gb|HO030975.1|HO030975
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|4289246|gb|AI441448.1|AI441448
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|193389928|gb|FK357585.1|FK357585
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAA-
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|6964283|gb|AW432976.1|AW432976
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATATGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|298168983|gb|HO020287.1|HO020287
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|208044561|gb|GD841041.1|GD841041
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|298164053|gb|HO013698.1|HO013698
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|151409001|gb|EV278809.1|EV278809
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|193348188|gb|FK311104.1|FK311104
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|208280986|gb|GE078874.1|GE078874
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAAGCGTTTCAGCCG
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAA-GCGTTTCAGCCG
EST: gi|193416036|gb|FK376670.1|FK376670
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|207820624|gb|GD791734.1|GD791734
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|193344828|gb|FK310404.1|FK310404
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
EST: gi|41145861|gb|CK606072.1|CK606072
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... ttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgggcatgattcccatcttatagcactgattctttttctctcttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA
                          cactgat  putative branch site (score: 3)
                          cactgattctttttct  CT-rich tract
                               attcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaattagttttggtattgataatgagatggaataggagcaaagttgttgggcatgattcccatcttatagcactgattctttttctctcttttattcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatct