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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataagatgatggggcacatgccttttttattaacagtttttatagttattttgaaatttatgtaatcacaatttgtttgactgaagttcctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTCCACAAGCTGGTGCGCCTCCAGCTCAAGCTTTTCCTCCTGCTACTGGCTG

Basic information

species Glycine max
transcript GLYMA08G17000.1
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|5606682|gb|AI900780.1|AI900780
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGAT
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGAT
EST: gi|193364936|gb|FK333193.1|FK333193
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|21676810|gb|BQ629161.1|BQ629161
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|58022037|gb|CX708778.1|CX708778
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|9900814|gb|BE609782.1|BE609782
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|208111416|gb|GD909134.1|GD909134
EST:     ACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: ACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|208311817|gb|GE109039.1|GE109039
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|23052768|gb|BU577259.1|BU577259
EST:     TCCACAACCAATCTCAACAACTCCTACTAACTGGACACCAGAAACAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAACTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|6719412|gb|AW307059.1|AW307059
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|192304648|gb|FG994940.1|FG994940
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|27425246|gb|CA936766.1|CA936766
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|22541018|gb|BU090861.1|BU090861
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|6952276|gb|AW424344.1|AW424344
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|15663310|gb|BI700681.1|BI700681
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|192304647|gb|FG994939.1|FG994939
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|58020333|gb|CX707075.1|CX707075
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
EST: gi|6846843|gb|AW349133.1|AW349133
EST:     TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTG                         CTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC
genomic: TCCACAACCAATCTCAGCAGCTCCTACTAACTGGACACCAGAAGCAGCTGgtacgaatta ... cctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattttgaaatttatgtaatcacaatttgtttgactgaagttcctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTCCACAAGCTGGTGCGCCTCCAGCTCAAGCTTTTCCTCCTGCTACTGGCTG
                               gtttgac  putative branch site (score: 4)
                                           ttcctcttac  putative PPT
          aaatttatgtaatcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataagatgatggggcacatgccttttttattaacagtttttatagttattttgaaatttatgtaatcacaatttgtttgactgaagttcctcttacagCTGCAGGAGATTGGGGTGAGGCTGTTCCAGCTCCTGCTCCAGCTCCAGTTCCACAAGCTGGTGCGCCTCCAGCTCAAGCTTTTCCTCCTGCTACTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - -gatgggg
- - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg