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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACTTGAATCTTCCCAGTTACACAGCAATGGAGAGGCTAATACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtgtagctaatgtaatttaagatttgatgcaaatttatgtctaagtgagatagccttgaaatttggatagctctgctctttttggaccggttcactgagcattttagcacaagcttaaaaggagatgtagctaccattatgcatatattagtgttcaagctaattctttcattactctttgcag

Basic information

species Glycine max
transcript GLYMA04G03080.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03080.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0001g13280.t01 (Vitis vinifera), 5'ss of exon 6
CACACTTGAATCTTCCCAGTTACACAGCAATGGAGAGGCTAATACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg--tagctaatgtaatttaagatttg-atgcaaatttatgtctaagtgag-atagccttgaaatttggatagctctgctctttttggaccggttcactgagcattttagcacaagcttaaaaggagatgtagctaccattatgcatatattagtgttcaagctaattctttcattactctttgcag
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CACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGACAACAGTAGTTAGACAATGCTTAAATCAAGAGCTTAGCAAGgtaatcttctatttgttatttttcctttgtgcgcgcgtgcgtgtgtgtgtgtgttggtgtgttttattgggattcttggaggcctgctcatgttggatta-----------------------------------------------------------------------------------------------
















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|15287071|gb|BI470962.1|BI470962
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|10252427|gb|BE820193.1|BE820193
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGNNGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|208275174|gb|GE067994.1|GE067994
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|254325124|gb|GR834549.1|GR834549
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|207704160|gb|GD685002.1|GD685002
EST:     GGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: GGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|193710804|gb|FK647767.1|FK647767
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|209723413|gb|BW679947.1|BW679947
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTC
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTC
EST: gi|209723414|gb|BW679948.1|BW679948
EST:     TAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|254325123|gb|GR834548.1|GR834548
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
EST: gi|13788314|gb|BG650906.1|BG650906
EST:     TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAG                         GATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA
genomic: TACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtg ... ctctttgcagGATGGGCCACCATTTTCCTTAAAGGATTTTCTCAAAAGTTGATGGAAAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACTTGAATCTTCCCAGTTACACAGCAATGGAGAGGCTAATACAGCAGGCTACAGTTGTAAGACAATGCTTAAGTCAAGAAGCTGGCAAGgtaatgggtgtagctaatgtaatttaagatttgatgcaaatttatgtctaagtgagatagccttgaaatttggatagctctgctctttttggaccggttcactgagcattttagcacaagcttaaaaggagatgtagctaccattatgcatatattagtgttcaagctaattctttcattactctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG