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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctttcagtattttctttttgtttgtattgtaacttgtaagagacactgttcaacttctttaaccataatcttcctttttacttctctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG

Basic information

species Glycine max
transcript GLYMA08G23930.2
intron # 2
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|4307032|gb|AI443989.1|AI443989
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGT-GTTATGCTTAGTAAG                         AGTAAAAACAT-AGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAA-CATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298198982|gb|HO042345.1|HO042345
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCCGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|192332023|gb|FK024539.1|FK024539
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|16348403|gb|BI973998.1|BI973998
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298178394|gb|HO024129.1|HO024129
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|16105282|gb|BI893022.1|BI893022
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|151410032|gb|EV279840.1|EV279840
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298171945|gb|HO021537.1|HO021537
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|27446142|gb|CA953265.1|CA953265
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298196834|gb|HO041577.1|HO041577
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298179084|gb|HO027555.1|HO027555
EST:     TAGAGAATAAGGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|120495849|gb|EH224016.1|EH224016
EST:     TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTAGTTATGCTTAGTAAG                         AGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacactgttcaacttctttaaccataatcttcctttttacttctctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG
                ctttaac  putative branch site (score: 3)
                            tcttcctttttacttc  putative PPT
                                  tttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctttcagtattttctttttgtttgtattgtaacttgtaagagacactgttcaacttctttaaccataatcttcctttttacttctctatttacagAGTAAAACATCAGGTTCTGCTGCAGCTTCATCTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT