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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatgactaattagtaagcattttgaagaatataatgtgttgcttgtgcttttgctctgaatactttctgcttacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCTCGGATATTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGACA

Basic information

species Glycine max
transcript GLYMA01G05080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 6
cacatgactaattagtaagcattttgaagaa----tataatgtgttgcttgtgcttttgctctgaatactttctgcttacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCTCGGATATTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGACA
   ||     ||||   | || |||  |       | ||  |||| |||||   | |     |    | || ||  |||  |     |    || |  ||||||    |||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||| ||||| |||||||||||||||||||| || || |
---attttggattaaagaacaatttataatggctttttatagtgtagcttgctttgtgagaatttgga-ttgctaattatgttgccttcctcttatgattgcagTCGCTGCTTTGTGACCCAAACCCAAACTCTCCTGCAAATTCAGAAGCAGCACGGATGTTTAGTGAGAACAAGCGTGAATACAACAGAAGAGTGCGTGAGA
















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|22933973|gb|BU551112.1|BU551112
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|14126011|gb|BG790449.1|BG790449
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|19452681|gb|BM954091.1|BM954091
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|19452497|gb|BM953907.1|BM953907
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|151402063|gb|EV271876.1|EV271876
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|19348294|gb|BM892826.1|BM892826
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
EST: gi|11273919|gb|BF324308.1|BF324308
EST:     ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT
genomic: ATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAGgtcacagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttttgctctgaatactttctgcttacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCTCGGATATTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGACA
                        tgcttac  putative branch site (score: 2)
                                          tttcttgtt  putative PPT
               aatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatgactaattagtaagcattttgaagaatataatgtgttgcttgtgcttttgctctgaatactttctgcttacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCAAATTCAGAAGCTGCTCGGATATTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGACA

-acatgac
- - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgagtt