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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCAAACTGGGCTATTCATAAATTCTTGTTTTGCTCATTGTCAGTCTGAGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctcaatttagatttccgttgtcttaggatatagataagtagtttggaaccactacctgtctattgccttgaataatcttaattgacatgtact...

Basic information

species Glycine max
transcript GLYMA10G27960.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G27960.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0005g02440.t01 (Vitis vinifera), 5'ss of exon 11
ATCTCAAACTGGGCTATTCATAAATTCTTGTTTTGCTCATTGTCAGTCTGAGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctcaatttag---atttccgttgtcttaggatatagataagt-agtttggaaccactacctgtct-attgccttgaataatcttaattgacatgtact---------------------------------------------------------------------
   ||||| |||||| ||||||||||| || |||||||| || ||| |||||  |||||| |||||||||||||||||||||||  || | |   | | |||||    |  ||||     |||    ||| | |      |  || | | ||    |||  | ||   || | || || || |   |||| | ||  | ||||                                                                       
TGATCAAAATGGGCTCTTCATAAATTCGTGCTTTGCTCACTGCCAGACTGAGTTACAGGATACATGGTTTGCTGATGACTCTCCTTTTCTTGGAAAAAGGgtatgccatagatttgatccattcattttgacattctccttccatgatttagagcagaattagtataagtttcatggctttcagccatctcatttccc-tgtatggttaaagactcggcacaatagaaggcatggaaattgaactctaaattaattaaattttcaatattgcag

upper sequence: GLYMA10G27960.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0005g02440.t01 (Vitis vinifera), 5'ss of exon 23
ATCTCAAACTGGGCTATTCATAAATTCTTGTTTTGCTCATTGTCAGTCTGAGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtata---------tgctcaatttagatttccgttgtctt---aggatatagataag---tagtttggaaccactacctgtctattgccttgaataatctta-attgacatgtact-----------------------------------------------------------
   ||| | ||| || ||||||||||| || |||| |||||| ||| ||||||||||||| ||||||||||||||||||||||||||||| |   | |||||||          || || ||| |  ||  |||| || |   | ||| |||| |||   ||||||  ||     |    | |    |||   ||   |    || |  | | |||                                                           
TGATCAGAATGGACTCTTCATAAATTCGTGCTTTGTTCATTGCCAGACTGAGAGACAGGATACATGGTTTGCTGATGACTCTCCCCTTATTGGAAAAAAGgtatgccatggatttgatccattcattttgacgttctccttccatgatttagagaagaattagtttttaagtttcatggctttcaaccctctcatttcccagcatggttaaggactaggcacaataggaggcatggaaattgaactctaaattaattcaattttcaatattgcag
















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|7589716|gb|AW705484.1|AW705484
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|209702071|gb|BW670555.1|BW670555
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|7030329|gb|AW460112.1|AW460112
EST:     TGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: TGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|14196191|gb|BE657978.2|BE657978
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|7285509|gb|AW597996.1|AW597996
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|192301335|gb|FG994043.1|FG994043
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACGAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
EST: gi|207679795|gb|GD661729.1|GD661729
EST:     AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAG                         CCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA
genomic: AGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctc ... tacgatgcagCCAATTGCAGTTGCTGTTGGAGACTGGTATTTTGATCGAGAAGTTGTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTCAAACTGGGCTATTCATAAATTCTTGTTTTGCTCATTGTCAGTCTGAGAGACAGGAGACATGGTTTGCTGATGACTCTCCCCTTATCGAGGACAAGgtatatgctcaatttagatttccgttgtcttaggatatagataagtagtttggaaccactacctgtctattgccttgaataatcttaattgacatgtact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT