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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCAAAGTGCTTAATGAACTGTGAAGTTGCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaattccttatcaagttcatggttatttaacacaaagatcctggtataatgttttctgatgctcttggaataattagtttttattacaatttg...

Basic information

species Glycine max
transcript GLYMA05G32260.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32260.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 2
AGGCAAAGTGCTTAATGAACTGTGAAGTTGCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaattccttatca----agttcatggt-tatttaacac--------aaagatcctggtataatgttttctgatgctcttggaataattagtttttattacaatttg----------------------------
||||||||||||||||||||||||||||  | ||||||||||||||||||| ||| |||||||| || |  || || ||||| ||||||||||||||||||| |||  ||||   | |||      ||||| || ||||   ||          ||||   | ||  | | || | || | ||  | |  || | | |   | ||  |  |||                            
AGGCAAAGTGCTTAATGAACTGTGAAGTCTCTTTGATTCTTGAGCACAAGTTTGAACAGCTTCAGCAAATCTCAGAGGATCCTATGAATCAAGTTTCTCAgtaagtataattgtgtttcatagagattcattgtatattagccatcatgaattgaagaatttagt-cagttttatatgttacttctaggttagtgaatcaatgttgaatattgttgaagaagttatgtttgctccttgcag

upper sequence: GLYMA05G32260.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0028g01400.t01 (Vitis vinifera), 5'ss of exon 3
AGGCAAAGTGCTTAATGAACTGTGAAGTTGCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagt-taaattccttatcaagttcatggttatttaacacaaagatcctggtataatgttttctgatgctcttggaataattagtttttattacaatttg
|||| || || || ||||| |||||||| ||  | |||||||| || |||||||| |||||||| ||||  || ||||||||  | |||||||||||||||||||| |  |  || | |  |  |  | |         | || |      ||  |   || |||||    | | |  |    | ||||    || |    
AGGCCAAATGTTTGATGAATTGTGAAGTAGCTGTTATTCTTGAACATAAGTATGAACAGCTTCAGCAGATGTCTGATGATCCATTAAATCAAGTTTCTCAgtgagtatttaacccgtgtatatattttagaccaacgttaaaagggcttatgtgcatgtttctctgaactccattgtttgtccatttttccccaccaaca-
















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|192320821|gb|FK013911.1|FK013911
EST:     TATGA-CAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAA-TCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|7591146|gb|AW706885.1|AW706885
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|15664606|gb|BI701977.1|BI701977
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGTTTTGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|209729464|gb|BW651831.1|BW651831
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCACATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|192323976|gb|FK015697.1|FK015697
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|213604131|gb|DB974229.1|DB974229
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|9899186|gb|BE608084.1|BE608084
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|213591496|gb|DB955760.1|DB955760
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|120533986|gb|EH262119.1|EH262119
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|18718067|gb|BM523023.1|BM523023
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|120534144|gb|EH262277.1|EH262277
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|9898920|gb|BE607888.1|BE607888
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|5509324|gb|AI855882.1|AI855882
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
EST: gi|192320820|gb|FK013910.1|FK013910
EST:     TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTTTCA                         GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA
genomic: TATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaa ... tctttctcagGGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCAAAGTGCTTAATGAACTGTGAAGTTGCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCAAGTTTCTCAgtgagttaaattccttatcaagttcatggttatttaacacaaagatcctggtataatgttttctgatgctcttggaataattagtttttattacaatttg

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT