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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGTAGCTTTACGCTGCACTGATCCTAATGCACAAAAGCGGCCTAAAATGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataatttctgctgaagttaatttcaacctcagagtagggctaattaatgcatagtgaggtatgcatatcatgtgtttgttctttaattaactgg...

Basic information

species Glycine max
transcript GLYMA11G05830.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05830.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 5'ss of exon 6
TCTTGTAGCTTTACGCTGCACTGATCCTAATGCACAAAAGCGGCCTAAAATGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgta-acaataatttctgct--gaagttaatttcaacctcagagtagggctaattaatgca--tagtgaggtatgcatatcatgtgtttgttctttaattaactgg
||| |||||| | |||||   |||||| ||  |||| |||||||| |||||||| ||||| ||||| ||||||||||||||||| ||||| | || ||| |||  ||   |||||| ||   || |||| |  ||  |   | |  |||  ||     |   ||   |  ||    || |       || |    || ||     
TCTCGTAGCTCTGCGCTGTGTTGATCCAAACTCACAGAAGCGGCCAAAAATGGGTCATGTTATACATATGCTTGAAGCTGAAGAATCCCCCTTCAGAGATgtatgcatccatttctactttaaatttaagtcaaatatggcacttaggcacatgtggactactaacaaattacatttaaccaacaaatgctaacaaaata-----
















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|213617268|gb|DB978950.1|DB978950
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|209723008|gb|BW668852.1|BW668852
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|213605481|gb|DB978818.1|DB978818
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|31475669|gb|CD417697.1|CD417697
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|6724952|gb|AW309351.1|AW309351
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|8826057|gb|BE209849.1|BE209849
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCANGACATTCACCTAATGATAGAGTANGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|58016385|gb|CX703127.1|CX703127
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|26048897|gb|CA785350.1|CA785350
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|9258343|gb|BE346490.1|BE346490
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
EST: gi|13240269|gb|BG359578.1|BG359578
EST:     TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAG                         GATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG
genomic: TGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataa ... ttacttacagGATCGCAGAGCTAAAAGGGATGCAGGACATTCACCTAATGATAGAGTAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGTAGCTTTACGCTGCACTGATCCTAATGCACAAAAGCGGCCTAAAATGGGGCATGTGATACACATGCTTGAAGCTGAAGATTCCCCTTACAAAGAGgtaacaataatttctgctgaagttaatttcaacctcagagtagggctaattaatgcatagtgaggtatgcatatcatgtgtttgttctttaattaactgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA