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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagcaatgggaggattataccaaaaaatataatgagtgtgttgtcattatggttagttaatctttgcg...

Basic information

species Glycine max
transcript GLYMA12G07740.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07740.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv06s0004g03450.t01 (Vitis vinifera), 5'ss of exon 11
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgta-atgccattctaactttgacataaataa-agtagcaatgggaggattatacca-aaaaatataatgagtgtgttgtcattatggttagttaatctttgcg
 ||||| || || || |||||||| || |||||||||||||| ||| ||||| ||||||| || ||||||||||| ||| |||| ||||| ||  ||||||||  | |  || |||| ||     |  |||  || | || |  ||   | ||  | ||||| |  || | | |||  | |  ||  ||  |  |  |||   
GTTTCTCTTTGCCGTGATGTTTGGGGATTGGGGTCATGGAATATGCTTGTTGTTGGGAGCATTAGTTCTTATAGCTCGTGAAAGTAAGCTTAGTTCTCAGgtatgttctgttataacattctagcatttaatggtggaaaagaaagtgctctattagaaaaacactat-attttgtaattagaattttttctccagttttt--

upper sequence: GLYMA12G07740.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 5'ss of exon 10
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagcaatgggaggattataccaaaaaatataatgagtgtgt-tgtca----ttatggttag-ttaatctttgcg-----------
 || || ||||| |||||||||||||||||||| |||||||| ||  |  | ||||| ||  |   |||| ||  |  | | |  || ||  | |   |||||||         |||||  |     | |  | |  ||   || ||   |     |  |  | |    || | | |||    || |||| |   ||| | |   |           
TTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGTTTACTTCTGGGGGCTCTTTATCTTGTATTAAATGAGAAGAAACTTGGGAGCAAGgtaatttttgaaagactttctctgcgctca--tggtcatttaagcatctcaagttgaccttcagttgaggtttgtctcaagttttgtggtgaaactaaacctgttggactgctgcag

upper sequence: GLYMA12G07740.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 5'ss of exon 10
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagca-atgggaggattat-----accaaaaaatataatgagtgtgttgtcattatggttagttaatctttgcg------------------------------------------------------------
||| || ||||| |||||||||||||||||||| |||||||| ||| |  | ||||| ||  |   |||  ||     | | |  || ||  | |   |||||||    ||||||  | || ||| ||      ||| |  | || ||  |     | | || ||| |  |   | ||||  ||| ||  |||      ||||||                                                             
ATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGCTTACTTCTGGGGGCACTTTATCTCGTATTGAATGAGAAGAAACTTGGAAGCAAGgtaatt---ttctaaagtgga-atatattcccctgcacacagtagaatccttggtgatctaagaatttt-tctttttgttcacatcatc-ttaacccccctttgcttcaagatttaggtgacatttgagatctgtgataacctaaaattcagaattgtaactgcag

upper sequence: GLYMA12G07740.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ12515 (Selaginella moellendorffii), 5'ss of exon 10
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagcaatgggaggattataccaaaaaatataatgagtgtgttgtcattatggttagttaatctttgcg
|||||| |||||||| |||||||| ||||||||||| ||||||  | || | |||| | |  |    ||  | | |    | || |  ||  | | ||||||     | ||     ||   | |    |   |   | |  |||  | | | ||                                              
ATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTCTTGCTCCTGGCAACTCTCTGGCTGCTTGTAAACGAGAGGAGACTTGGAAGTCAGgt----tcgtttggttttcctcttcttcagtcttttattctgagcttaaaaacag---------------------------------------------

upper sequence: GLYMA12G07740.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ10256 (Selaginella moellendorffii), 5'ss of exon 10
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagcaatgggaggattataccaaaaaatataatgagtgtgttgtcattatggttagttaatctttgcg
|||||| |||||||| |||||||| ||||||||||| ||||||  | || | |||| | |  |    ||  | | |    | || |  ||  | | ||||||     | ||     ||   | |    |  ||   | |  |||  | | | ||                                              
ATTTCTATTCGCGGTCATGTTTGGAGACTGGGGTCACGGAATTGTCTTGCTCCTGGCAACTCTCTGGCTGCTTGTAAACGAGAGGAGACTTGGAAGTCAGgt----tcgtttggttttcctcttcttcagtgttttattctgagcttaaaaacag---------------------------------------------

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|193453457|gb|FK418169.1|FK418169
EST:     TGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAG                         CGACTTGGAAGCTTTATGGAGATGCTATTTGGTGGGCGTTATGTGCTACTT
genomic: TGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccat ... tttctgccagCGACTTGGAAGCTTTATGGAGATGCTATTTGGTGGGCGTTATGTGCTACTT
EST: gi|254315253|gb|GR830246.1|GR830246
EST:     TGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAG                         CGACTTGGAAGCTTTATGGAGATGCTATTTGGTGGGCGTTATGTGCTACTT
genomic: TGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccat ... tttctgccagCGACTTGGAAGCTTTATGGAGATGCTATTTGGTGGGCGTTATGTGCTACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGCCTGTTGCTGGGAGCGTTGGTTCTTATAGCACGTCAAAGCAAGCTCAGCACTCAGgtaatgccattctaactttgacataaataaagtagcaatgggaggattataccaaaaaatataatgagtgtgttgtcattatggttagttaatctttgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaata