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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacttaactaagtagttccttgttcattaattgtatccagtatttactttgctttgtcttctttctgtctctaattataatacgtatttatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTCGTATTCATTCGAGATTCTTACGGTTGTCTTACCTGCTGGGAGTCAGTTT

Basic information

species Glycine max
transcript GLYMA20G35300.2
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|208253383|gb|GE051119.1|GE051119
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|22933553|gb|BU550692.1|BU550692
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|208181496|gb|GD978459.1|GD978459
EST:     GGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: GGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|207710978|gb|GD694028.1|GD694028
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|207771889|gb|GD745660.1|GD745660
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTG
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTG
EST: gi|207763761|gb|GD737478.1|GD737478
EST:     CCTCGGAGGAAGAGTAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: CCTCGGAGGAAGAG-AAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|208186588|gb|GD982667.1|GD982667
EST:     CCTCGGAGGAAGAGTAAGACCTTAAGTAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: CCTCGGAGGAAGAG-AAGACC-TAAG-AAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|254342793|gb|GR858955.1|GR858955
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|193513489|gb|FK467789.1|FK467789
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|208301695|gb|GE100367.1|GE100367
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAGGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|193345486|gb|FK313009.1|FK313009
EST:     AGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGA-TTGTC
genomic: AGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|22522770|gb|BU081581.1|BU081581
EST:     ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: ATGCTCACAAGCCTCGGAGGAAGAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
EST: gi|208055300|gb|GD854535.1|GD854535
EST:     GAGAAGACCTAAGAAGAAAAAGAAGCAG                         GTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC
genomic: GAGAAGACCTAAGAAGAAAAAGAAGCAGgtttattact ... tatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactttgctttgtcttctttctgtctctaattataatacgtatttatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTCGTATTCATTCGAGATTCTTACGGTTGTCTTACCTGCTGGGAGTCAGTTT
                         ctctaat  putative branch site (score: 3)
                                           tttatcctcc  putative PPT
                          tctaattataatacgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacttaactaagtagttccttgttcattaattgtatccagtatttactttgctttgtcttctttctgtctctaattataatacgtatttatcctccagGTGTAGGCATGATGGCTAAACTGAGCAGTAGAATGAGCAATTGGATTTGTCGTATTCATTCGAGATTCTTACGGTTGTCTTACCTGCTGGGAGTCAGTTT

- - - - - - - - -ttccttg