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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag

Basic information

species Glycine max
transcript GLYMA10G01280.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttt-tgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag------
||| | |||||||| ||| | || || || ||||||||||| || ||||| |||||||  |||||||| ||||| ||||||||||||||||||||||||  | ||  | || || ||   | || ||||  | |||||| |   |   |  |  || ||  |   ||||  | || |       
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagcttt-cctttttttttaccaccag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 5'ss of exon 9
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgta----ttataatgttatttttgcatgtct-atttacat-gttatttcattatgatattcatatatatatgaaccttcatcttcag------------------------------------------------------
||  | ||||| ||||||||||||||||||||    |||||||| || || || ||||  || || || ||||| ||||||||||||||||||||||||       | |  ||  |||||    ||| |||| ||  |||| |   |  || |    || |||| || |   |   | |||                                                        
GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAGgtaggagccttcacatttattttgttcctcttattttcagagttaatgtctcctgcttactatttataaattataatgtgtattctaattatgcatactttcaccagatctttcataaaagaatgccatctgaagctgtag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g19150.5 (Oryza sativa), 5'ss of exon 10
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtatta----taatgttatttttgcatgtct-atttacat-gttatttcattatgatattcatatatatatgaaccttcatcttcag--------------------
||  | ||||| ||||||||||||||||||||    |||||||| || || || ||||  || || || ||||| ||||||||||||||||||||||||  |    | |  ||  |||||    ||| |||| ||  |||| |   |  || |    || |||| || |   |   | |||                      
GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAGgtaggagccttcacatttattttgttcctcttattttcagagttaatgtctcctgcttactatttataaattataatgtgtattctaattatgcatactttcaccag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 10
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag--------------
||| | || || || ||| | |||||||| |||||||||||||| |||||||||||||  ||||| || ||||| ||||||||||||||||| ||||||     || || | || |  ||| |     |   |  | ||  ||  |  | ||   |  |    | ||||   |   |              
GTTCTGGGCACACCCACACGTGAAGAAATTAAGTGCATGAATCCAAATTATACCGAGTTTAAATTCCCGCAAATCAAAGCTCACCCATGGCATAAGgta--gggattttgtattggattgtgtgccctctcttcctgtcccta--acctccaccaaggttgacatcttccattgatgtctttctgtgctag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 10
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag---------------
||||| || ||||||||||| || ||||| |||||||||||||| ||||| || || |  ||||| |||||||||||||| |||||||||||||||||| |  |  |        | || |   || |  | |  | |  || | | |  |  |   ||||  |  |||||  | |                
GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAGgtactggatagaagca---ggatattacttcaattctgctatgcttcttacaacctcacgaatattgattttcattcttattgtacctcctatcag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgt-ctatttacatgtta---tttcattatgatattcatatat--atatgaaccttcatcttcag-----------------
|| || || || || ||  | || || || |||||||||||||| || || || |||| ||| ||||| ||||| || |||||||| |||||||| ||||     || | ||| || |||  || ||| ||| ||    |||  |  ||   | || |  |  | ||| ||   | | ||                    
GTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAAgtat----gtggtctttgtgaatgcactgtttccatcttgggctttggtagtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgagcggtgggttt

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgt-ctatttacatgtta---tttcattatgatattcatatat--atatgaaccttcatcttcag-----------------
|| || || || || ||  | || || ||||||||||||||||| || || || |||| ||| ||||| ||||| || ||||||||||||||||| ||||     || | | | || |||  || ||| ||| ||    |||  |  ||   | || |  |  | ||| ||   | | ||                    
GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtat----gtggtctgtgtgaatgcactgttttcatcttgggctttggtagtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgtgagcggtgggt

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatg-tctatttacatgttatttcattatgatatt-catatatatatgaaccttcatcttcag-----------------
|| || || || || ||| | || || || |||||||||||||| || || || |||| ||| ||||| |||||||| ||||| || ||||||||||||         | | | |   || |||  |    || | |     | |  | |  ||  |   |   || | | | ||  |                  
GTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAGgtacggctggtctgtgtgttagtggtctggtatggtgctttggagatgtactgtaacagttgattggaaagcgttacctgtattcataataacggtgatt

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgtctatttaca-tgttatttcat-tatgatattcatatatatatgaaccttcatcttcag------------------------------------------------------------------------------------------------------------
|| ||||| || || ||| | || || || |||||||||||||| || || || |||| ||| ||||| |||||||| |||||||| |||||||||||||  |  |||   ||| |  |  ||||||  | || | | | || ||   |  |   |  |||  |   | ||    |  |                                                                                                            
GTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAGgtatggtt-tgtatgtttgggttagctatttttagtggtctattatataatttgataggaattatccgtgtcctcgatattggtgattttgaatttggttggttggacgctgctactcgttgtgattgggagaatggagcgtgttgcattgaccttagcaacgtgcgaattgattggttctgtggtggcag

upper sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtat---tataatgttatttttgc-atgtctatttacatgtta---tttcattatgatattcatatatatatgaaccttcatctt-cag--------------------------------------------------------------------------------------------
||||| || || || ||  | || || ||||||||||||||||| || || || |||| ||| ||||||||||| || || ||||| |||||||| ||||   | |  ||  | |  |   |||||    |   ||||    ||  | |  | || |   || |   | | ||||  || |  ||                                                                                            
GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagt-ggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag

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|208323313|gb|GE125650.1|GE125650
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|208280495|gb|GE075023.1|GE075023
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|151393723|gb|EV263598.1|EV263598
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|208161219|gb|GD961741.1|GD961741
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
EST: gi|193328222|gb|FK294243.1|FK294243
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGG
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGG
EST: gi|19944926|gb|AB082946.1|AB082946
EST:     ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG                         ATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA
genomic: ATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataat ... tcatcttcagATCTTTCACAAGCGCTTACCTCCTGAGGCTGTGGATCTCGTCTCAAGGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttttgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag

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