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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtttgacaatatctttttatgatgagtataatgcatttattattttcattatacttgatagaagtagaattgattagaatcttgaacattatc...

Basic information

species Glycine max
transcript GLYMA20G38630.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38630.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 5'ss of exon 5
AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtttg-acaatatctttttatgatgagtataatgcatttattattttcattatacttgatagaagtagaattgattagaatcttgaacattatc-----------------------------------------------------------------------------------------
||| || || | ||||||||| || |||||||| || |||||||| ||||| ||  |||| || || || ||||| ||||| ||||||||||| ||||||||| |   | ||  |  ||| | | | |  | |  |       |   ||    ||||||||   | |           | | || ||| |||||     |                                                                                          
AGTTAAGCTAAAAATGCAAGGTGCCTGCAGTGGATGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttctgtgctttatttctgtttcctcaaaacctccactccttttggctcattatataaggtgttttatctgataagtaaaatgttgaaagaagttgcaattcctattagtttgttcagactgcttaaagcagtaatttatcctttgatctagcgaaattttaatatttcacacttctttggcag

upper sequence: GLYMA20G38630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaa--caagtttgacaatatctt----tttatgatgagtataatgcatttattattt--------tcattatacttgatagaagtagaattgattagaatcttgaacattatc--------------------------
||| || |||||||||||||| || || || || || ||||||||||| || ||| ||||||| || ||||| |||||||| |||||||||||| | |||||||  |   |  |   || || |    ||||| ||   | | || | |||  | ||         |||| || |||| ||  |||  | |    | |     | | |||||                            
AGTGAAGCTTAGAATGCAAGGAGCTTGTAGCGGTTGTCCAAGTTCATCTGTTACTTTGAAATCCGGAATTGAGAATATGCTTATGCATTATGTTTCCGAGgtaaagctgataaggagatgtcctaccatttatcatttctgttattcttttgctgttgagggagaatcatgat-cttgttaatagtctactc---ttgttctctaatcattactcaccaaagcgtttgtgcaaaacacag

upper sequence: GLYMA20G38630.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0106g00620.t01 (Vitis vinifera), 5'ss of exon 5
AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaa--gtttgacaatatctttttatgatgagtataatgcatttattattt-tcattatacttgatagaagtagaattgattagaatcttgaacattatc
||| ||||| | ||||||||| ||||| ||||||||||| || ||||| || || |||||||| ||||||||||||||||||||||| ||||| |||||||||||||   || |    |    || ||   | | | |  |  |      ||   ||| | | |       || | |  |  ||| |  | |||   |||   
AGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCACTATGTACCTGAGgtaacaatcattagtttctgcacttatagattcattgtggtctaacatgaatgcatcaatgtgcacccatcaaattgtgtgtatt-gtgtattgcgtattt--

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|193412381|gb|FK381308.1|FK381308
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193544966|gb|FK504299.1|FK504299
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193630552|gb|FK584105.1|FK584105
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193659389|gb|FK605972.1|FK605972
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAGAGGTGTGGAACAAGAATTGGATGCTGA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGA
EST: gi|193411504|gb|FK381579.1|FK381579
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193392603|gb|FK358762.1|FK358762
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|208051204|gb|GD846707.1|GD846707
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193448629|gb|FK413354.1|FK413354
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATG
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATG
EST: gi|192327952|gb|FK021699.1|FK021699
EST:     TGACTCTGAAATCAG-CATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAG-TGTGGA-CA-GA-TTGGATGCTGAG-ATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193328310|gb|FK294331.1|FK294331
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAAGGTGTGGAACAAGAATTGGATGCTGAGGATGATGGAGCAGCATTA
EST: gi|193338444|gb|FK303385.1|FK303385
EST:     TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAG                         GTCAAAAGGTGTGGAAACAAGAATTGGATGCTGAGGATGATGGAGCAGCAT
genomic: TGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtt ... acattttcagGTCAAA-GGTGTGGAA-CAAGAATTGGATGCTGAGGATGATGGAGCAGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCATTATGTTCCTGAGgtaacaagtttgacaatatctttttatgatgagtataatgcatttattattttcattatacttgatagaagtagaattgattagaatcttgaacattatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT