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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatttgcctgtccatttatgtgatatttcattgtgatattcatatatatgaaccttcattatcag

Basic information

species Glycine max
transcript GLYMA02G01220.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatt-tgcctgtccatttatgtgatatttcattgtgatattcatatata-tgaaccttcattatcag------
||| | || ||||| ||| | || || || ||||| ||||| || |||||||||||||| |||||||| ||||| |||||||| |||||||| ||||||    ||  | || || ||   | |  ||||| |  ||||| |  ||   |  |  || ||     ||||  || | |       
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag

upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 5'ss of exon 9
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgta-----ttgtaatgttatatttgcctgtccatttatg----tgatatttcat-tgtgatattcatatatatgaaccttcattatcag----------------------------------------------------
||  | || || || |||||||||||||||||   ||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||| ||||||      |  |   |||| ||   |     ||||       | || | || |   |  |||| ||| ||   ||  |  ||| | |                                                     
GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAGgtaggagccttcacatttattttgttcctcttattttcagagttaatgtctcctgcttactatttataaattataatgtgtattctaattatgcatactttcaccagatctttcataaaagaatgccatctgaagctgtag

upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g19150.5 (Oryza sativa), 5'ss of exon 10
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgta-----ttgtaatgttatatttgcctgtccatttatg----tgatatttcat-tgtgatattcatatatatgaaccttcattatcag------------------
||  | || || || |||||||||||||||||   ||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||| ||||||      |  |   |||| ||   |     ||||       | || | || |   |  |||| ||| ||   ||  |  ||| | |                   
GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAGgtaggagccttcacatttattttgttcctcttattttcagagttaatgtctcctgcttactatttataaattataatgtgtattctaattatgcatactttcaccag

upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 10
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatttgcctgtccatttatgtgatatttcattgtgatattcatatatatgaaccttcattatcag----------------
||| | || || || ||| | |||||||| ||||| |||||||| ||||| |||||||| ||||| || ||||| |||||||| |||||||||||||||  |  || || |||| |  |||              | ||  |   |  | ||   |  |  || |     ||                   
GTTCTGGGCACACCCACACGTGAAGAAATTAAGTGCATGAATCCAAATTATACCGAGTTTAAATTCCCGCAAATCAAAGCTCACCCATGGCATAAGgta--gggattttgtattggattgtgtgccctctcttcctgtcccta--acctccaccaaggttgacatcttccattgatgtctttctgtgctag

upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 10
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatt-tgcctgtccatttatgtgatatttcattgtgatattcatatatatgaaccttcattatcag---------------
||||| || ||||| ||||| || ||||| ||||| |||||||| |||||||| || || ||||| |||||||||||||| || |||||||| |||||| || |  |    |   |     | || || ||  ||  ||| ||   |   |||   ||||  |  |||||| | |                
GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAGgtactggatagaagcaggatattacttcaattctgctatgcttc-ttacaac-ctcacgaatattgattttcattcttattgtacctcctatcag

upper sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatttgcc----tgtccatttatgtgata---tttcattgtgatattc-atatatatgaaccttcattat-cag--------------------------------------------------------------------------------------------
||||| || || |||||  | || || |||||||| |||||||| || ||||| |||||||| ||||||||||| || || || || ||||| || ||||  |  |  |     |||     ||||    |  ||| |    ||  | || | || |  || |   | | ||||  |  |  ||                                                                                            
GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag

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|193455275|gb|FK419252.1|FK419252
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|193667331|gb|FK608071.1|FK608071
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|15286220|gb|BI470111.1|BI470111
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|10254836|gb|BE822602.1|BE822602
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|298195934|gb|HO044325.1|HO044325
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|9901022|gb|BE609988.1|BE609988
EST:     TTACACGGAGTT-AAATTTTCACAGAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: TTACACCGAGTTCAAATTTCCACA-AATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|16349285|gb|BI974880.1|BI974880
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|207820675|gb|GD792526.1|GD792526
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|207797958|gb|GD768522.1|GD768522
EST:     TACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: TACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|13791263|gb|BG653854.1|BG653854
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTTTTTTGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|207749260|gb|GD720090.1|GD720090
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|7590534|gb|AW706284.1|AW706284
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|208218102|gb|GE016120.1|GE016120
EST:     TACTACCGAGTTCTAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: TAC-ACCGAGTTC-AAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|13562753|gb|BG550973.1|BG550973
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|9259545|gb|BE347700.1|BE347700
EST:     ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGCGTTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|37994511|gb|CF806247.1|CF806247
EST:     ATTACACCGAGTTCAAATTTCCACACATTAAAGCTCATCCATGGCATAAG                         ATATTTCACAAGC
genomic: ATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaat ... tcattatcagATATTTCACAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatttgcctgtccatttatgtgatatttcattgtgatattcatatatatgaaccttcattatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA