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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaccaaactttctagaacagtgtatgtatacgctgatacttgcaaaggagtctcttatgttcatttcattttattctcaccaactttattttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTGAGGAGCAGGCTGAATTGCAGCAAGTCCTTGAACTTCAAGAAAGAAGGCT

Basic information

species Glycine max
transcript GLYMA01G43700.1
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|9901264|gb|BE610232.1|BE610232
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|208085774|gb|GD882406.1|GD882406
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|7042736|gb|AW472630.1|AW472630
EST:     TTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTAGTGATT-CCATCTTG                         GGGCAAGGATGTT
genomic: TTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTA-TGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTT
EST: gi|15202990|gb|BI425758.1|BI425758
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|9819986|gb|BE555499.1|BE555499
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|6915919|gb|AW397449.1|AW397449
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|208326619|gb|GE124921.1|GE124921
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG
EST: gi|7146570|gb|AW508492.1|AW508492
EST:     TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTG                         GGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAACAATTG
genomic: TTTAAGCCCCTCTGGCTTTGGCTCTAAAGAACCTTATGATTTCCATCTTGgtaatcaaat ... ttttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggagtctcttatgttcatttcattttattctcaccaactttattttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTGAGGAGCAGGCTGAATTGCAGCAAGTCCTTGAACTTCAAGAAAGAAGGCT
                              ttctcac  putative branch site (score: 2)
                                        ctttatttt  putative PPT
           ttatgttcatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaccaaactttctagaacagtgtatgtatacgctgatacttgcaaaggagtctcttatgttcatttcattttattctcaccaactttattttatgcagGGGCAAGGATGTTGTATAATCCACATGATATCTTATTGAGAAGAAAAATTGAGGAGCAGGCTGAATTGCAGCAAGTCCTTGAACTTCAAGAAAGAAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - ccaaact
- - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - -gctgata
- - - - - - - - - - - - - - - - - - - - cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accaact