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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTAGGATCAATAAGAGATATGCACCTTAAAGAGTCTGAAGCATCTGGAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaaacatggaagctgcaagtcttttaatttccaactaggatacaataaatgaccaagtaaagcagggctcataggatttttggctagtttata...

Basic information

species Glycine max
transcript GLYMA13G18470.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18470.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0005g03440.t01 (Vitis vinifera), 5'ss of exon 5
AGAGCTAGGATCAATAAGAGATATGCACCTTAAAGAGTCTGAAGCATCTGGAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaaacatggaagctgcaagtcttttaatttccaactaggatacaataaatgaccaagtaaagcagggctcataggatttttggctagtttata------
  |||| |||||||||||||| ||||| || |||| |||||||  |||||| ||||||||||||||||| || || ||||||||||| |||||||| |||||| | | |||      |  |  || |    |||  |    |||  ||    | |||    ||||   |     ||  || | |||||     |     |      
GCAGCTTGGATCAATAAGAGAGATGCAGCTAAAAGTGTCTGAATTATCTGGGAAAATTAGTGGGCTTGAAAAAAAGATTCAATATGCAGAGATTGAGAAGgta-atttaaattctatacttttaattgaactaaagtttgtcta--attgtttgaattgataagtt--gtcattcttttaag-tttttaatatgacggcaatgggt
















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|208293142|gb|GE096392.1|GE096392
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAAATTT
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATTT
EST: gi|193571522|gb|FK531857.1|FK531857
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTC
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTC
EST: gi|16346177|gb|BI971772.1|BI971772
EST:     GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAAATTTGAGCCAAGNNNNNNNGACCATC
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATTTGAGCCAAGAAAAAAAGACCATC
EST: gi|208022836|gb|GD821350.1|GD821350
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAAATTTGAGCC
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATTTGAGCC
EST: gi|208166870|gb|GD961288.1|GD961288
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAAATT
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATT
EST: gi|208260587|gb|GE059385.1|GE059385
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAA-TTTGAG
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATTTGAG
EST: gi|207710757|gb|GD691735.1|GD691735
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAGTATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTT
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTT
EST: gi|208187414|gb|GD982224.1|GD982224
EST:     GAAAAATTAGTGGACTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAG                         CGAAGCATTGAAGATAAACTTTCAAATTTGA
genomic: GAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaa ... attttgccagCGAAGCATTGAAGATAAACTTTCAAATTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTAGGATCAATAAGAGATATGCACCTTAAAGAGTCTGAAGCATCTGGAAAAATTAGTGGGCTTGAGAAGAAAATTCAATATGCTGAGATTGAAAAGgtacaatcaaacatggaagctgcaagtcttttaatttccaactaggatacaataaatgaccaagtaaagcagggctcataggatttttggctagtttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG