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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttttaagctagttacttttgaaatttagaatgttactagttactgattgctagtaatcattttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAATCTAAGAAGTGTCATGGATAT

Basic information

species Glycine max
transcript GLYMA04G05910.1
intron # 9
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|193355512|gb|FK322939.1|FK322939
EST:     ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
EST: gi|208328618|gb|GE130826.1|GE130826
EST:     ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
EST: gi|193306549|gb|FK269703.1|FK269703
EST:     ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
EST: gi|208238277|gb|GE039925.1|GE039925
EST:     CTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: CTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
EST: gi|193374951|gb|FK339889.1|FK339889
EST:     ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: ATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
EST: gi|193438022|gb|FK403147.1|FK403147
EST:     TTGGTTCTATTCCTTCTTCCATTGGTGACTTTGGAACATCTTCTGAAGTT                         GAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA
genomic: TTGGTTCTATTCCTTCTTCCATTGGTGAC-TTGGAACATCTTCTGAAGTTgtgagtcttt ... attttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgaaatttagaatgttactagttactgattgctagtaatcattttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAATCTAAGAAGTGTCATGGATAT
                           tactgat  putative branch site (score: 2)
                                           tcatttt  putative PPT
       aaatttagaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttttaagctagttacttttgaaatttagaatgttactagttactgattgctagtaatcattttgctagGAATCTGAGCAGAAATCATTTAACAGGGTTTATTCCAGCAGAATTTGGAAATCTAAGAAGTGTCATGGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA