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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC

Basic information

species Glycine max
transcript GLYMA12G04460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G073571_T03 (Zea mays), 3'ss of exon 5
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatga-tacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
                                                                           ||  ||  |   ||      | |  |||  | |      | || ||   ||   || | ||   |   ||| |  |   | |||||||| | ||||||||||||| | |||||||| || || ||  |||| |||||||||||||| ||||| |||||||||||||| || ||  | ||||| |
--------------------------------------------------------------------------gtatgagcctc--aattcatttttacactttgttgctgtttttttcttgcttggaatatattgggttaatttgtcgtatctccagACTCTATACCAAATGTTTATCGTCAATGCTGGTCCGGGCTTCCGGTTACTATGGAACACTGTGAAGTCCTTCCTTGATCCCAAAACGACCGCCAAGATAC

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
                                                                   |||||   | |   |||||| |      | | |  |   || |    | |||||  |    ||| ||   ||  ||| ||  ||  | |||||||| | ||||||||||||  | |||||||| || || ||  || | |||||||||||||| ||||| || ||||||||||| || ||  | ||||| |
------------------------------------------------------------------gtatgagcctcattttttttacac-----tctcttttgttgttt----ttttgct--tggaatatattgggttaatttgttgcatc-tccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
                                                               ||  ||   ||||  |  || |      |  |  ||  || |||| ||||    |||| || ||   ||| |  | | |          || |||||||||  |||||||||||| || ||||| || |||||||||||| | || |||||||||||||||   || ||||| || |||||| || | || ||||
---------------------------------------------------------------gtattagttaattggagcttct------aatacttgatctcaggtatcaa---atgctaatcttggctttgtggtatttc---------atgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgtt-ttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
                                    |||   ||  ||  | ||||  | ||  | |||| |   | |    |||  |||     ||| ||       | |   |     |||  | || |          || | || | || | ||||||||||||||||||||||| || |||||||| ||||| |||||| |||| ||||||||||| ||| |||| || |||||||| |||||||| |||||||
----------------------------------gtattcaacctttttctgttgacatgataagctata-gttgtaatccatttcaaaattgatataggtgactgaatatgtgcc----ctggatcttgaa---------ctctcttaactgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC

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|193724403|gb|FK657985.1|FK657985
EST:     GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAAATGCTGGCCC
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCC
EST: gi|193320737|gb|FK283122.1|FK283122
EST:     GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAAAATAGACTAGGCCCTGGATTTAG
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAAA-T-G-CT-GGCCCTGGATTTAG
EST: gi|193481751|gb|FK446870.1|FK446870
EST:     GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTA
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTA
EST: gi|193399516|gb|FK363069.1|FK363069
EST:     GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTA
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTA
EST: gi|151397966|gb|EV267839.1|EV267839
EST:     GGGATCTCATTATGCGGTTACAAA-GATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAG-TTGCTA
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTA
EST: gi|207760411|gb|GD731382.1|GD731382
EST:     GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATCATAA
genomic: GGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaaca ... aatgatacagACTCTCTGCCAAATGTTTATCATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
                                         ttttaat  putative branch site (score: 3)
                    ttttttattttttatt  CT-rich tract
        aactattgctgatttt  TA-rich tract