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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatggtttgacttattatatattttgaaaatatacattatgttccttcctgttagtatatctttaatcctttggcctgacgcactcaaaattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG

Basic information

species Glycine max
transcript GLYMA08G42300.1
intron # 5
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|208256562|gb|GE054829.1|GE054829
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTCGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|207694669|gb|GD676528.1|GD676528
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCA
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCA
EST: gi|6665849|gb|AW277299.1|AW277299
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|298164275|gb|HO013920.1|HO013920
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACTTTGTTTGCTGATGTGGAGTTCATGCAAAAGCG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCG
EST: gi|17020848|gb|BM091882.1|BM091882
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|8285076|gb|BE022635.1|BE022635
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|208288479|gb|GE086144.1|GE086144
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|6666384|gb|AW277843.1|AW277843
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGANACATTGTTTGCTGATGTGGAGTTCATGCANAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|193662744|gb|FK604008.1|FK604008
EST:     ACTTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTG
EST: gi|193716892|gb|FK654660.1|FK654660
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|9985912|gb|BE659918.1|BE659918
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|298186356|gb|HO036989.1|HO036989
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTCGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|193443430|gb|FK409190.1|FK409190
EST:     TAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: TAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|193362589|gb|FK324909.1|FK324909
EST:     TAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: TAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|298198572|gb|HO040111.1|HO040111
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|208274341|gb|GE071123.1|GE071123
EST:     AGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: AGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|207820397|gb|GD792851.1|GD792851
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAAACATTGTTTGCTGATGTAGGAGTTCATGCAA
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAA-CATTGTTTGCTGATGT-GGAGTTCATGCAA
EST: gi|298181551|gb|HO025726.1|HO025726
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTCGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|207720734|gb|GD701777.1|GD701777
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
EST: gi|6454914|gb|AW185524.1|AW185524
EST:     ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAG                         CATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
genomic: ACCTCGAGGGTAGATTGGAGAAAGGATTAAGCAGAGTTAGATCTAGAAAGgtgtatacat ... aattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcctgttagtatatctttaatcctttggcctgacgcactcaaaattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG
                              gcctgac  putative branch site (score: 3)
        ttagtatatctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatggtttgacttattatatattttgaaaatatacattatgttccttcctgttagtatatctttaatcctttggcctgacgcactcaaaattttgcagCATGAAACATTGTTTGCTGATGTGGAGTTCATGCAAAAGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG