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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggttagtatttgatatattttaccaaaataatgctgtggaatatttatgttacgtctgttttctttttcttgctttattttgataaaaatattatttttcctggactatctttaactttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAGGACTGACACTGC

Basic information

species Glycine max
transcript GLYMA18G46830.1
intron # 6
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|58022185|gb|CX708926.1|CX708926
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|6848327|gb|AW350617.1|AW350617
EST:     GCTTGCCGGAGTGNCCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|151406125|gb|EV275940.1|EV275940
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|192315950|gb|FK008833.1|FK008833
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|58025369|gb|CX712110.1|CX712110
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|193360773|gb|FK326425.1|FK326425
EST:     AATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: AATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|193608634|gb|FK562380.1|FK562380
EST:     ACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: ACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|20497875|gb|BQ272805.1|BQ272805
EST:     GTGACCATCCCACNTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|151411748|gb|EV281559.1|EV281559
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAA
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|192331285|gb|FK023782.1|FK023782
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACCG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|33389737|gb|CA852944.1|CA852944
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAG
EST: gi|213587116|gb|DB959537.1|DB959537
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTA
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTA
EST: gi|192331284|gb|FK023781.1|FK023781
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACCG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAA
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAA
EST: gi|192301669|gb|FG997611.1|FG997611
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAAGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|6725773|gb|AW310172.1|AW310172
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|6566253|gb|AW233934.1|AW233934
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|21887980|gb|BQ741193.1|BQ741193
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|151398479|gb|EV268350.1|EV268350
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|58022451|gb|CX709192.1|CX709192
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|58017891|gb|CX704633.1|CX704633
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
EST: gi|57575865|gb|CX548836.1|CX548836
EST:     GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTG                         GTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG
genomic: GCTTGCCGGAGTGACCATACCACCTGAAAGAATATATGGCCTTGGAACTGggttagtatt ... tttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttattttgataaaaatattatttttcctggactatctttaactttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAGGACTGACACTGC
                                      ctttaac  putative branch site (score: 3)
                                            ctttactt  CT-rich tract
     attttgataaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttagtatttgatatattttaccaaaataatgctgtggaatatttatgttacgtctgttttctttttcttgctttattttgataaaaatattatttttcctggactatctttaactttacttacaGTCCTAAGGTAGAAGTTCTGAAGCAGCTACAGAAAAAGCCAGAGCACCAAGGACTGACACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA