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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccacaaagtgtttgtgaaaatgctgctgtgaggaggaaacttggacaccatacctgtgtatgtttaattaaccaaagttattttgttgttcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGAACCACCAAAACCCCCGCCGATTTCCTCAAATCCATTCGTGGGAGGCCGG

Basic information

species Glycine max
transcript GLYMA18G46370.1
intron # 1
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|193684145|gb|FK622681.1|FK622681
EST:     AATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGGAAGCAGGATCAGGA
genomic: AATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|192324452|gb|FK015803.1|FK015803
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|151410204|gb|EV280019.1|EV280019
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|151407789|gb|EV277604.1|EV277604
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|193428401|gb|FK396681.1|FK396681
EST:     GAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTG-TTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: GAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|193654271|gb|FK596517.1|FK596517
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAAGATAAAAATGAGCGGAAC
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGA-GATAAAAATGAGCGGAAC
EST: gi|9901469|gb|BE610437.1|BE610437
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|207785641|gb|GD757390.1|GD757390
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAAATGAGCGGAACAGAGAAAGCAGGATCAGG
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGAT-AAAAATGAGCGGAACAGAGAAAGCAGGATCAGG
EST: gi|4396101|gb|AI495098.1|AI495098
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|192327084|gb|FK015476.1|FK015476
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
EST: gi|208158322|gb|GD956885.1|GD956885
EST:     AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAG                         GTGCTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA
genomic: AAGAGAAGAGACAGTGAATCGCGGTTTCAATTCAACCCACTTCATCTCAGgtaccccctt ... tcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaccatacctgtgtatgtttaattaaccaaagttattttgttgttcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGAACCACCAAAACCCCCGCCGATTTCCTCAAATCCATTCGTGGGAGGCCGG
                     aattaac  putative branch site (score: 2)
                                    ttttgttgttccttt  putative PPT
                  tttaattaaccaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccacaaagtgtttgtgaaaatgctgctgtgaggaggaaacttggacaccatacctgtgtatgtttaattaaccaaagttattttgttgttcctttgaagGTGTTTGAAGTTGAGATAAAAATGAGCGGAACAGAGAAAGCAGGATCAGGAACCACCAAAACCCCCGCCGATTTCCTCAAATCCATTCGTGGGAGGCCGG

-ccacaaa
- - - - -tgtttgt
- - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - gaggagg
- - - - - - - - - - - - - - - - - - - - cttggac
- - - - - - - - - - - - - - - - - - - - - - - - ccatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaa