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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaaaatatttttgatcacttgcaacctgtgctatttattcatgcggccttcacgcaattttgtacttgaatgttaaagtggctttcctctacttttcctttttacctcttaaaagggggcttacaaaatgcaaagtttgtaagtgattacatttacatgtctgggtgcag

Basic information

species Glycine max
transcript GLYMA11G11490.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11490.1 (Glycine max), 5'ss of exon 15
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 5'ss of exon 15
AGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaaaatatttttgatcacttgcaacctgtgctatttattcatgcggccttcacgcaattttgtacttgaatgttaaagtggctttcctctacttttcctttttacctcttaaaagggggcttacaaaatgcaaagtttgtaagtgattacatttacatgtctgggtgcag
 ||||| |||| ||| ||||| |||||  ||||||||||||||||| | |||||||| || |||||| |  | |||||||| || || |||||||| |||||||  |     ||||| ||   |   |  |           | | |||| |    |  |    ||| | | |||     ||| |  | | ||  || |||||  |    |                                                                  
TGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGTTGAATCCAAAGTTGACCATTGTGAGAAAGgtat-aactcggtatttatgccaatcagttataaaacactggtgtgcatgtg----tagcatggtttcgaagttg-----taatggtgttctctcctgcttttggtaaacag-----------------------------------------------------------------
















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|22933713|gb|BU550852.1|BU550852
EST:     CTCCTGGTGGACTNGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|17400311|gb|BM177093.1|BM177093
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|7028762|gb|AW458545.1|AW458545
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|11275017|gb|BF325341.1|BF325341
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCATAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|15814707|gb|BI786982.1|BI786982
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|23732846|gb|BU764597.1|BU764597
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|11274082|gb|BF324450.1|BF324450
EST:     CGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
EST: gi|208175474|gb|GD976869.1|GD976869
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCAT
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCAT
EST: gi|10843371|gb|BF066672.1|BF066672
EST:     CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAG                         CTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA
genomic: CTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaa ... ctgggtgcagCTTTCATCAAGTGCAGCTAATGCTTCATCTAATGGGAACGGTCCTTCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTCTAAATCCAAAATTAACGATTGTGAGGAAGgtattgaaaaaatatttttgatcacttgcaacctgtgctatttattcatgcggccttcacgcaattttgtacttgaatgttaaagtggctttcctctacttttcctttttacctcttaaaagggggcttacaaaatgcaaagtttgtaagtgattacatttacatgtctgggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA