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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaacttatgttattgttactcccatctcccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG

Basic information

species Glycine max
transcript GLYMA12G09540.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 6
--------------gtattcaacttatgttattgttactcccatct---cccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
               |  |  |   |    | |   | |     ||   |   |||   | | ||  |     |   |  | |   |||||| ||||| |||||||||||||| |||||||| |||||||| ||  ||||  | || ||||| |||||||| ||  | || ||| | |||||||||||||
gtaagctccgaatgattctggagggaaagaaattacatttttggctgaacatgtttggcatatgtcaaccttattgaaaatttgaaacagGCAGCTGTCGCTGTTCAAGCAGGAGTATGTGTAGACATATTTGCTATAACCGACGAATACACCGATTTGGCTTCGTTGAAGTTTTTAAGTATTGAAAGTG

upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g33690.1 (Oryza sativa), 3'ss of exon 6
gtattcaacttatgttattgttactc--ccatctcccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
    | |   | ||| ||| || |||    |  | | |     |   ||   |     | |   |  ||| ||||||||||  |||||||||||||||||||||||| ||| | || ||  | |||||||| ||||| ||| |  | ||| | ||| |||| ||| |||| || |
---gtaagtctctgtaatttttgctcaataaattacaagaatattctagaatatatcctaattggcatatcacagGCTGCTAGTGCTGTTCAAGCAGGTGTATGTGTGGACCTTTTTGCAATTACAAATGAATACACAGATCTTTCTTCCTTGAAAGTTCTTAGTGTTGAGAGCG

upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G141735_T01 (Zea mays), 3'ss of exon 6
----gtattcaacttatgttattgttactcccatctcccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
    | ||    || |  ||    ||         | |  | |  | | | ||     ||||| |  || |  |||||| ||||||||||||||  |||| |||||  | |||||||| || |||||  |||| |||||||||||||| || || || ||| | ||||| |||||||
gtaagcatgagtctaaaatttaaattcgatttgatttctctgttat-gtactgatcttattgaaaattgaa--acagGCAGCTGTTGCTGTTCAGTCAGGAGTATGCATAGACATATTTGCTGTAACTGATGAATACACTGATTTGGCTTCACTGAAGTTTTTAAGTATCGAAAGTG

upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G27460.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtattcaacttatgttattgttactcccatctcc-catttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
       | |  | | | | || |  ||||    |    || | ||   ||   | ||  | ||   | | ||| ||||  |  ||||||| ||| ||||||||||||| ||  |||| || || |||||||||||||| ||||| |||||||| || || || || ||||||||||
gtaagtcttatttcaagattttctgtctccggaatggatatattctttgagctta-gatctaacggctcttttatagGCCACCATTGCTGTCCAATCAGGTGTATGTGTAGATTTATTTGCAGTTACAAATGAGTACACAGATTTAGCATCCCTGAAGTTCCTTAGCATTGAAAGTG

upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0080g00510.t01 (Vitis vinifera), 3'ss of exon 6
------gt-attcaacttatg--ttattgttactcccatctcccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
      || ||   | ||||   ||||| || ||    |      |||      |    ||  |||||||  | | | |||||||||||| ||||||||||||||||| ||||| || ||||| || || ||||| ||||| || ||||||||||||||||||||||| |||||||||||||
gtaattgtgatctgaattattatttattttttctttagttggatgtttttgtagaacataaacattgacacatatttcacagGCTGCTGTCGCTGTTCAAGCAGGTGTTTGTGTGGATATATTTGCTGTTACAAACGAGTATACGGATTTGGCATCCCTAAAATTTCTTAGTATTGAAAGTG

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|16996632|gb|BM086004.1|BM086004
EST:     ATCGTGCTTTACTCCCGGAGCAGACACCCTTTTATAAAGATCTG                         GCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACA
genomic: ATCGTGCTTTACTCCCGGAGCAGACACCCTTTTATAAAGATCTGgtattcaact ... tgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttactcccatctcccatttcctagaagtggaagaattgacatgtgtattacagGCTGCTGTTGCTGTTCAAGCAGGTGTATGTGTTGACATATTCGCCGTAACAAATGAGTACACTGATTTGGCATCCCTAAAATTTCTGAGTATTGAAAGTG
                                   aattgac  putative branch site (score: 3)
                                aagaatt  TA-rich tract