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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgttttgtagtttggaaaaaatttgtcaggatgtatgtgcatttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
---tgttgttttgtagtttggaaaaaatttgtcaggatgtatgtgcat-ttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC
   |||    |||    |||    | |   |  |    ||    |||  || |||| ||   |   ||||||  ||   ||   ||||  ||| ||   | |||||||| || || |||||  |||| ||||| || || ||||| || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||||||
gcatgtaaacttg--acttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattg--ctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC

upper sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 16
--tgttgttttgtagtttggaaaaaatttgtcaggatgtatgtgcat--ttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC
     ||        || || ||||  || | ||  || |||| |||  |   | ||||  |  |       |   | ||  ||  |||  ||| ||| | |||||||| || || |||||||||||||||  |||||| || ||  |||| ||||||||||||||||| || || |||||||| |||||||| ||||| ||
ttcactggaaaactattagggaaaa--ttattagc-tgcatgtccatgatccctttatttttcctctttcacaaaaggtctatttctgat-ttgattactgcagCTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCC
















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|57575927|gb|CX548898.1|CX548898
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58021805|gb|CX708546.1|CX708546
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACNTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACNTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58018020|gb|CX704762.1|CX704762
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACNTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58020232|gb|CX706974.1|CX706974
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58024542|gb|CX711283.1|CX711283
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACNTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|8286121|gb|BE023680.1|BE023680
EST:     CTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: CTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|51345142|gb|CO985875.1|CO985875
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC
                                        ccttgttt  CT-rich tract
                            atcatttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgttttgtagtttggaaaaaatttgtcaggatgtatgtgcatttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- -tgttttg
- - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - tatgtgc