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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatagagaatctttaactggtgtctgttcattagtaactctaggctattttctgggaagctgatatcattcttgtaatttttttgttcactatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCAGGTGTATTCATAGGAAATGTGAAGGTTCTTGTGCGGTTGTCTTTTGGAC

Basic information

species Glycine max
transcript GLYMA12G04820.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 17
gaatagagaatctttaact-ggtgtctgttcatt--agtaactctaggctattttctgggaagctgatatcattcttgtaatttttttgttcactatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCAGGTGTATTCATAGGAAATGTGAAGGTTCTTGTGCGGTTGTCTTTTGGAC
   ||     |  ||| |  ||| |    | |||        | ||   ||  |    |||||||||     |||      || | || ||     | | ||||| || ||||| |||||   |||||||||||||||||| || ||  |||| |||||||||||||| ||| |||| || ||||| ||||| || |||||| 
--ttatttgctggttagccaggtattgagttattttgtcttgtttaccatacctctctggaagctgaaccttttccccctgttctgtt-ttggtggtgttcagGGCACAGAGGTTGTCCCTAGCAATTCAAGGTCACACACGTGTTTACTGTCTGGTGTATTCATAGGCAATATGAAAGTGCTTGTTCGGTTATCATTTGGAA
















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|208270545|gb|GE065759.1|GE065759
EST:     CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAG                         GGAACTGAGGTAGTCCCGCCCAATTCAAGGTCACACACATGCTTGTTGTCA
genomic: CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAGgtaagccaat ... ctatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCA
EST: gi|18041035|gb|BM309329.1|BM309329
EST:     CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAA                         GGAACCGAGGTAGTCCCA
genomic: CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAGgtaagccaat ... ctatttgcagGGAACCGAGGTAGTCCCA
EST: gi|193382838|gb|FK347715.1|FK347715
EST:     CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAG                         GGAACCGAGGTAGTCCCACCCAATTCAA
genomic: CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAGgtaagccaat ... ctatttgcagGGAACCGAGGTAGTCCCACCCAATTCAA
EST: gi|13311361|gb|BG405012.1|BG405012
EST:     CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAG                         GGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCA
genomic: CTGAAGCTGTAAATACCGTCATTAATCTTCTTGGGATGCAGCCTTGTGAGgtaagccaat ... ctatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattttctgggaagctgatatcattcttgtaatttttttgttcactatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCAGGTGTATTCATAGGAAATGTGAAGGTTCTTGTGCGGTTGTCTTTTGGAC
             agctgat  putative branch site (score: 4)
                                 tttttttgttcact  putative PPT
                  atatcattcttgtaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatagagaatctttaactggtgtctgttcattagtaactctaggctattttctgggaagctgatatcattcttgtaatttttttgttcactatttgcagGGAACCGAGGTAGTCCCACCCAATTCAAGGTCACACACATGCTTGTTGTCAGGTGTATTCATAGGAAATGTGAAGGTTCTTGTGCGGTTGTCTTTTGGAC

- - - - - - - - - tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagctg