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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgcatgaaatcaatccacttcttgcgcttgttgttagattatacatgattactattagctgcattttctattctaacttccaatggacctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTATCCCCAACACGGTTGAATCTACTTCTTTTTTAGATGCTTGCAACCTATT

Basic information

species Glycine max
transcript GLYMA08G18780.3
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|6454198|gb|AW184811.1|AW184811
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
EST: gi|298189446|gb|HO037849.1|HO037849
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
EST: gi|192332181|gb|FK023830.1|FK023830
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
EST: gi|27425344|gb|CA936864.1|CA936864
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
EST: gi|31310639|gb|CD395842.1|CD395842
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
EST: gi|13481470|gb|BG510813.1|BG510813
EST:     TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTG                         CACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA
genomic: TTGTAAAGAGCTGGCTAGTAAATTCAACCTTAAAATGATTCGAGCCATTGgtatgatgta ... ctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgattactattagctgcattttctattctaacttccaatggacctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTATCCCCAACACGGTTGAATCTACTTCTTTTTTAGATGCTTGCAACCTATT
                           ttctaac  putative branch site (score: 1)
                                            cctctgt  putative PPT
                   attttctattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgcatgaaatcaatccacttcttgcgcttgttgttagattatacatgattactattagctgcattttctattctaacttccaatggacctctgtgcagCACTTGTTTTGATGGAACATCTCAAGGCTGAGATAAAAGGTTCATCACTTATCCCCAACACGGTTGAATCTACTTCTTTTTTAGATGCTTGCAACCTATT

- -gcatgaa
- - - - - - caatcca
- - - - - - - - - - ttcttgc
- - - - - - - - - - - - - -gcttgtt
- - - - - - - - - - - - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttcca