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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttactatatttcagggtttttattttcatcaaaccaaaatttaagagtgctatgagaaaagttcttaataaggtctgtggtgtgctgtgatttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAGTCATCTGGTTCACCTGATCCGGTTCCATTATCTTCCCTGGCTGCAAAAT

Basic information

species Glycine max
transcript GLYMA12G36990.1
intron # 4
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|31306733|gb|CD391936.1|CD391936
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|6847768|gb|AW350058.1|AW350058
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|214009533|gb|DB990119.1|DB990119
EST:     GATTCTGTAGGAAAGGATACACAT-AA                         GGAACTGTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCA
genomic: GATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCT-TTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCA
EST: gi|31456494|gb|CD398522.1|CD398522
EST:     GTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGCCAG
genomic: GTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|21600620|gb|BQ610951.1|BQ610951
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|193599809|gb|FK550694.1|FK550694
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|192312797|gb|FK003995.1|FK003995
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGAGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|31463696|gb|CD405724.1|CD405724
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|192312798|gb|FK003996.1|FK003996
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGAGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
EST: gi|58019861|gb|CX706603.1|CX706603
EST:     GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAG                         GGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG
genomic: GCAATGGAGTTGAAGTAGTCTATGATTCTGTAGGAAAGGATACATTTGAGgtagtactta ... atttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgctatgagaaaagttcttaataaggtctgtggtgtgctgtgatttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAGTCATCTGGTTCACCTGATCCGGTTCCATTATCTTCCCTGGCTGCAAAAT
                  tcttaat  putative branch site (score: 3)
                                              tttgtcc  putative PPT
            aaaagttcttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactatatttcagggtttttattttcatcaaaccaaaatttaagagtgctatgagaaaagttcttaataaggtctgtggtgtgctgtgatttgtccagGGATCTTTGGCATGCTTGAAGCTTAGGGGCTACATGGTAAGTTTTGGGCAGTCATCTGGTTCACCTGATCCGGTTCCATTATCTTCCCTGGCTGCAAAAT

- - - - - - - gggtttt
- - - - - - - - - - - - - - -tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg