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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctctaactgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagttttatccaatcttatcatgtccactgtttccttg...

Basic information

species Glycine max
transcript GLYMA01G43540.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 5'ss of exon 5
TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta-actgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagttttatccaatcttatcatgtccactgtttccttg
 |||||||| || ||||| ||||| |||||||| || |||||| | || |||||||| ||||||||||||| ||| |||   ||||  ||||| ||||||||| | | |  | ||    ||| |||  |  |  || || | | ||           |   |    | || |   || | |   ||     |  || | | 
CCCAAACAACCTTATGCCCTTTGTGCAGCAAGTTGCTGTTGGCAGGCGACCTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACTGGGgtatgttttccattgttagaaagttactctattcaacttctacttgtttgttggctgtttttagtctgtttttagatgtcacattgatatataattgcat-

upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 5
TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta-actgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagtt--ttatccaatcttatcatgtccactgtttccttg
 |||||||| || ||||| ||||| |||||||| || |||||| | || |||||||| ||||||||||||| ||| |||   ||||  ||||| || |||||| | | |  | || |   |  ||| |   |  |  | ||   |       |    ||  |  | ||  ||||  | |   ||  |||  ||| ||   |  
CCCAAACAACCTTATGCCCTTTGTGCAGCAAGTTGCTGTTGGCAGGCGACCTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttgcattgtcagcatattacgttattcatctctttggttatttgcatgtgtgtctagatttgcttatgtagtaa-atattgtgaactattaaat--

upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 5
lower sequence: EFJ35039 (Selaginella moellendorffii), 5'ss of exon 5
TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctctaactgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagttttatccaatcttatcatgtccactgtttccttg
 ||||||||||| ||||| |||||||| ||||||||||| ||  || | || |  |||||||| ||||| || || ||    || || || || || ||||| |  ||| | ||  ||   ||    || |    || ||   || | |   ||    ||||   | ||| |   ||| |                    
CCCAAACAATCTGATGCCGTTTGTTCAACAAGTAGCAGTCGGAAGAAGACCCGAGCTGACAGTGTTTGGGAACGACTACCCAACGAGAGACGGAACAGGGgt-cagtctcaatgcttttttttatcacatt----ttattttctgtacattgaatgctcatggtttcttacc---tctgacggcag--------------

upper sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 5
lower sequence: EFJ17435 (Selaginella moellendorffii), 5'ss of exon 5
TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctctaactgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagttttatccaatcttatcatgtccactgtttccttg
 ||||||||||| ||||| |||||||| ||||||||||| ||  || | || |  |||||||| ||||| || || ||    || || || || || |||||  |    ||   | ||   ||||| |||  |  || ||   || | |   ||    ||||   | ||| |   ||| |                    
CCCAAACAATCTGATGCCGTTTGTTCAACAAGTAGCAGTCGGAAGAAGACCCGAGCTGACAGTGTTTGGGAACGACTACCCAACGAGAGACGGAACAGGGgtcagtctcaatgcattt---tttat-cac--attttattttctgtacattgaatgctcatggtttcttacc---tctgacggcag--------------

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|12490049|gb|BG043570.1|BG043570
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTACCATATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|209713128|gb|BW653837.1|BW653837
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|192299883|gb|FG990091.1|FG990091
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|22933171|gb|BU550310.1|BU550310
EST:     AATGATTATAATACAAGTGATNNNACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: AATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|9898582|gb|BE607550.1|BE607550
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|193517169|gb|FK473409.1|FK473409
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|57574123|gb|CX547098.1|CX547098
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|12489618|gb|BG043139.1|BG043139
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTATCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
EST: gi|57574248|gb|CX547223.1|CX547223
EST:     CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGG                         GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctcta ... tttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAAACAATCTCATGCCATTTGTTCAGCAAGTAGCAGTTGGCCGACGGCCTGCACTGACAGTTTTTGGAAATGATTATAATACAAGTGATGGCACTGGGgtacgctctaactgacttaaatttatgcactgaaatttttccatggaaaagaaaattgcatgaagttttatccaatcttatcatgtccactgtttccttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaga