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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgtttaggtgattttatgctttaggtggtatgtggattccaatacataaataaattggtttcactttaacaatgttccttttcttggtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAACTACTTGAGTTGTGGGAAGGAAACACCCCAAATCTCAATGATAAAGATC

Basic information

species Glycine max
transcript GLYMA20G29950.2
intron # 3
splice site 3'
intron type U2

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|21600588|gb|BQ610919.1|BQ610919
EST:     TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|192321496|gb|FK012874.1|FK012874
EST:     TGGCTGCTGGTGTCTTGCCTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|16343545|gb|BI969140.1|BI969140
EST:     TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|193509021|gb|FK466065.1|FK466065
EST:     TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|213588142|gb|DB984229.1|DB984229
EST:     TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACTTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|209715393|gb|BW684691.1|BW684691
EST:     TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: TGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
EST: gi|207797196|gb|GD771162.1|GD771162
EST:     GTCTGCTTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA
genomic: G-CTGC-TGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgt ... gtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacataaataaattggtttcactttaacaatgttccttttcttggtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAACTACTTGAGTTGTGGGAAGGAAACACCCCAAATCTCAATGATAAAGATC
                      ctttaac  putative branch site (score: 3)
 ttccttttcttggttt  putative PPT
 taaataaattggttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgtttaggtgattttatgctttaggtggtatgtggattccaatacataaataaattggtttcactttaacaatgttccttttcttggtttatgtagGTGCCTTCTACTTTGGGACCTGTAGTTGTGATCTCTTGGATGAAAAGGGAACTACTTGAGTTGTGGGAAGGAAACACCCCAAATCTCAATGATAAAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA