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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgggatcaatttctctgtacctgtgttagaaattttgtaatttattttcctatcgatcaatgtattttacttttcaagcatcactgccaatttgcaccatcctttaaaatgcctaatatttttgtgcacttaatgaag

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G157043_T02 (Zea mays), 5'ss of exon 7
GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgggatcaatttctctgtacctgtgttagaaattttgtaatttattttcctatcgatcaatgtattttacttttcaagcatcactgccaatttgcaccatcctttaaaatgcctaatatttttgtgcacttaatgaag
|| || ||||||||||||||||  ||||| ||||||||||| |||| |||||   |  |   |||| | || |  ||  || ||     ||||| | |  ||  |  | |   ||    ||||  |  |||  ||                                                            
GTCCTTGGAAACAAGTACCAAACTAAATTACTTGAAATAATCGATGGCAGgt---taggatctcaaatcctgttaactagttttctg--ttttg-attccatcctaatgtttttc----tattccatgttttcag------------------------------------------------------------

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 2
GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgggatcaatttctctgtacctgtgttagaaattttgtaatttattttcctatcgatcaatgtattttacttttcaagcatcactgccaatttgcaccatcctttaaaatgcctaatatttttgtgcacttaatgaag
||||| || ||||| |||||||| ||  |||||||||||||||| |||||||| || |   |||   | || ||      | |      |||| | | ||  | || ||| ||| | |||  || | || | ||  ||                                                         
GTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAGgtagatgttcaatctgctactttgaggggattt-----gttttcttaattgatctcttat-gattattgt--ttcatttgtaaaaaatgctcag---------------------------------------------------

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G171354_T05 (Zea mays), 5'ss of exon 1
--------------------------------------------------GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgggatcaatttctctgtacctgtgttagaaattttgtaatttattttcctatcgatcaatgtattttacttttcaagcatcactgccaatttgcaccatcctttaaaatgcctaatatttttgtgcacttaatgaag
                                                  ||||| || ||||| |||||||| ||  |||||||||||||||| |||||||| || |   |||   | || ||      | |      |||| | | ||  | || ||| ||| | |||  || | || | ||  ||                                                         
TTTTTTCTTGATAACATTGCTTAATGTCTAAGGTATTCTTATGTTTTTAGGTTCTTGGGAACAAATACCAAAGTAAGCTGCTTGAAATAATTGACGCCAGgtagatgttcaatctgctactttgaggggattt-----gttttcttaattgatctcttat-gattattgt--ttcatttgtaaaaaatgctcag---------------------------------------------------

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|193399157|gb|FK361719.1|FK361719
EST:     TGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
genomic: TGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
EST: gi|193720487|gb|FK657395.1|FK657395
EST:     GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCNGGGAGGTACCTGTA
genomic: GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTA
EST: gi|193511296|gb|FK470371.1|FK470371
EST:     TTCTCGGAAACAAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTA
genomic: TTCTCGGAAACAA-GTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTA
EST: gi|13181204|gb|BG352544.1|BG352544
EST:     CAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
genomic: CAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
EST: gi|18040573|gb|BM308867.1|BM308867
EST:     GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
genomic: GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
EST: gi|193350410|gb|FK315356.1|FK315356
EST:     TGAAATAATTGATTGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTAGCAGATCAGGGT
genomic: TGAAATAATTGA-TGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGT-GCAGATCAGGGT
EST: gi|208266803|gb|GE061918.1|GE061918
EST:     GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGG
genomic: GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGG
EST: gi|193347330|gb|FK313104.1|FK313104
EST:     TGAAATAATTGATTGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTG
genomic: TGAAATAATTGA-TGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTG
EST: gi|15813836|gb|BI786111.1|BI786111
EST:     GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
genomic: GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
EST: gi|193419797|gb|FK382425.1|FK382425
EST:     TGAAATAATTGATGCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
genomic: TGAAATAATTGATGCCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTGG
EST: gi|193339980|gb|FK306237.1|FK306237
EST:     TGAAATAATTGATTGTCCAG                         TGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTG
genomic: TGAAATAATTGA-TG-CCAGgtacatttgg ... cttaatgaagTGAGTTGCCAGAATTTCTGGGAGGTACCTGTACCTGTGCAGATCAGGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTCGGAAACAAGTACCAAAGCAAATTGCTTGAAATAATTGATGCCAGgtacatttgggatcaatttctctgtacctgtgttagaaattttgtaatttattttcctatcgatcaatgtattttacttttcaagcatcactgccaatttgcaccatcctttaaaatgcctaatatttttgtgcacttaatgaag

- - - - - - - - - - AAGCAA