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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttttatatatgcttctttctattagattatttcagcagccgtatttgattgaattttgtagataaaaatgatattcacttcagatcttcattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGAAATTAGTAGTGCAGATGAACTGACCCTAACAGAGCTCATGTTCAATGGT

Basic information

species Glycine max
transcript GLYMA08G47700.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 12
tgacttttatatatgcttctttctattagattatttcagcagccgtatttgattgaattttgtagataaaaatgatattcacttcagatctt----cattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGAAATTAGTAGTGCAGATGAACTGACCCTAACAGAGCTCATGTTCAATGGT
    |||  |||     ||| |  |||    |     |      ||  || | ||| |     | || |  |||  |         ||||||     | | ||| || |  ||||||||||| || ||||| || || |||| ||||||||||||||| |||||||| |||||  |||| || || ||||| ||||||||||| 
----tttcttattaaactctcttaatttagctgaaaaattgtttgttgttaaatgattagaagaaatcatgatgtcaacatgcctggatcttattttacttcagGTATGTCACAAGTGACAACGTTGTGGAGTTGAAGGGGAAGGTTGCTTGTGAAATCAGTAGTGCGGATGAGTTGACTCTCACGGAGCTTATGTTCAATGGG
















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|208145405|gb|GD941840.1|GD941840
EST:     GCCTTCAAGGATGAACTTAAGGCAAGAAAGAGAGTTCTTCGTAGGCTCGG                         ATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGA
genomic: GCCTTCAAGGATGAACTTAAGGCAAGAAAGAGAGTTCTTCGTAGGCTCGGgtaatgaaac ... ttcattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGA
EST: gi|192296445|gb|FG989105.1|FG989105
EST:     GCCTTCAAGGATGAACTTAAGGCAAGAAAGAGAGTTCTTCGTAGGCTCGG                         ATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGA
genomic: GCCTTCAAGGATGAACTTAAGGCAAGAAAGAGAGTTCTTCGTAGGCTCGGgtaatgaaac ... ttcattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgattgaattttgtagataaaaatgatattcacttcagatcttcattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGAAATTAGTAGTGCAGATGAACTGACCCTAACAGAGCTCATGTTCAATGGT
 atttgat  putative branch site (score: 5)
                                           tcttcatt  putative PPT
      attgaattttgtagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttttatatatgcttctttctattagattatttcagcagccgtatttgattgaattttgtagataaaaatgatattcacttcagatcttcattgcagATACGCTACAAGTGACAATGTAGTGGAATTAAAAGGGAGGGTTGCTTGTGAAATTAGTAGTGCAGATGAACTGACCCTAACAGAGCTCATGTTCAATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - gcagccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa