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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatgttcggaaaacgctttaatctgcttcgttttgttcggagaaaaaaaaaactgtgttgtagcggtgcttgagtttgaaactaacttgctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAAATCATGCACGCTCCAGTTCTAGTTCTCA

Basic information

species Glycine max
transcript GLYMA09G28650.2
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|207680009|gb|GD663189.1|GD663189
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAG                         TGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|209722479|gb|BW682829.1|BW682829
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTC--                         -------AGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|208065074|gb|GD867120.1|GD867120
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAG                         TGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|209725416|gb|BW658278.1|BW658278
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAG                         TGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|209711120|gb|BW676339.1|BW676339
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTC--                         -------AGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|213590193|gb|DB970061.1|DB970061
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAG                         TGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|209700495|gb|BW660895.1|BW660895
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAG                         TGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
EST: gi|213618229|gb|DB972999.1|DB972999
EST:     TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTC--                         -------AGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA
genomic: TCTCCCTTGCCGCTTCCGGCACCGAACGAACAGTCTCCGGCCAACTTCAGgtaactcaca ... gctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaactgtgttgtagcggtgcttgagtttgaaactaacttgctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAAATCATGCACGCTCCAGTTCTAGTTCTCA
                                    aactaac  putative branch site (score: 1)
                                          cttgcttt  CT-rich tract
                               tttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatgttcggaaaacgctttaatctgcttcgttttgttcggagaaaaaaaaaactgtgttgtagcggtgcttgagtttgaaactaacttgctttgctagTGAATTTAGCTCTTGCGTGCGAAAATTCTCGGAATATTTTGAATCCAGGAAATCATGCACGCTCCAGTTCTAGTTCTCA

- - - - -ggaaaac
- - - - - - - - - - - - ctgcttc
- - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaactaa