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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttatagcacctgatttcacag

Basic information

species Glycine max
transcript GLYMA12G01080.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01080.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G133624_T01 (Zea mays), 5'ss of exon 4
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttatagcacctgatttcacag-----------------------------------------------------------------------------------
||| |||||  | |||||||| || || || |||||||| || || | ||||||  | |||||||||||||| |||||||| ||||||||    ||||| |||||   | |      ||  |    |     || |  | |    ||||||  |     ||  | ||                                                                                   
AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaacaaa-ggtctactgcctccaccccacattatgattcacttatattattcttttgaagagtaggctgagattattcatattggttagcattacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcag

upper sequence: GLYMA12G01080.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccat-taaattatggatggctgtggacttggttagatgcttatagcacctgatttcacag---------------------------------------------
||  |||||  | ||||||| ||| |||||||| ||||||||||| | |||||| ||  | ||||| || ||  | ||||| |||||||||||||| || |||||||      || |  ||       |||   |||    ||| |  |  |   ||    || |                                                
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatc--ttgtttccttaccaagacgactccacatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag

upper sequence: GLYMA12G01080.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 5'ss of exon 5
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccattaaattatggatggctgtggacttggt-tagatgcttatagcacctgatttcacag--------------------------------------------------------
 || |||||  | |||||||| || ||||| || |||||||| || | ||||||| |  | |||||||||||||| ||||||||||||||||| ||||| ||||||| |   |   | |||  |  |    |  |   | | | || ||   || |   | ||||  |                                                        
GGGCTATGGGAAAGAAGGAAGTTTTTCTTTCCCGAATGTTCCGCCTATGGCAGATATTTTGTATGAAGTTGAGCTTATTGGCTTTGATGAAACTAAAGAGgtaagtttctcct---tcatgattttccaaagtttctttattgctgtttcctgc-ctaaacttcattgtatgcgagctcattatagaattcaatatatgaacctacaagcaacgcatgttacag

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|208146379|gb|GD946678.1|GD946678
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAA
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAA
EST: gi|208241398|gb|GE043238.1|GE043238
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
EST: gi|8825928|gb|BE209658.1|BE209658
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
EST: gi|208152853|gb|GD949160.1|GD949160
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
EST: gi|207790870|gb|GD759655.1|GD759655
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATA
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATA
EST: gi|192324546|gb|FK018702.1|FK018702
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
EST: gi|193440790|gb|FK405579.1|FK405579
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
EST: gi|207828640|gb|GD800499.1|GD800499
EST:     CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAA                         GGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC
genomic: CAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgcc ... gatttcacagGGGAAAGCTCGCAGTGATATGACTGTGGAGGAAAGAATTGGTGCAGCAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGATATGGAGAGGAAGGAAGCTTCTCTTTTCCAAATGTTCCACCCAAGGCAGATTTAGTTTATGAAGTTGAGCTCATTGGCTTTGATGAAACAAAAGAAgtaagttgccattaaattatggatggctgtggacttggttagatgcttatagcacctgatttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA