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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttgacatacttcctctcgcatttgtttgtgacctagacagtgtagttaaactggttcaatgcattgactatgcaatacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG

Basic information

species Glycine max
transcript GLYMA12G30540.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
-gtcttg-acatacttcctctcgcatttgtttgtgacctagacagtgtagttaaactggttcaatgcattgactatgca-atacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG
  || |  ||  |   | |  |  | |        |   |       |  ||| | | ||  |        | |||    |||   |||   |    |||||  || | ||||| || ||||||||||| || || ||||||||||| || || |||||||| |||||||||
actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG

upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 18
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 17
gtcttgacatacttcctctcgcatt----tgtttgtgacctagacagtgtagttaaactggttcaatgcattgactatgcaatacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG
   |||    | | |   |  ||||    ||||    || || ||  | |||||       || ||   |   | | | |  |  | | || ||| || ||||  |||| ||||| |||||||||||||| || || ||||| |||||||| || || |||||||||||||||
--gttggtgcagt-cgcattacattgcaatgttcaatacttatactttctagtttcga-aattgaagttaaaaagtctcc--ttttcaattgttggat-agGTACTGTTGATGTCTCTAAAAGCTGGTGGCGTTGGGATAAATCTAACAGCTGCGTCCAATGCTTTTGTCATG
















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|193508871|gb|FK465467.1|FK465467
EST:     AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG                         GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
genomic: AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTGgtcttgacat ... cttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
EST: gi|207838025|gb|GD810359.1|GD810359
EST:     AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG                         GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
genomic: AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTGgtcttgacat ... cttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
EST: gi|207694182|gb|GD674277.1|GD674277
EST:     AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG                         GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
genomic: AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTGgtcttgacat ... cttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
EST: gi|208307393|gb|GE107071.1|GE107071
EST:     AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG                         GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
genomic: AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTGgtcttgacat ... cttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCA
EST: gi|207771108|gb|GD743871.1|GD743871
EST:     AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG                         GTGTTGTTAATGTCACTAAAAG
genomic: AGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTGgtcttgacat ... cttgcatcagGTGTTGTTAATGTCACTAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtagttaaactggttcaatgcattgactatgcaatacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG
                      cattgac  putative branch site (score: 3)
                                      cttatttctt  putative PPT
                                  aatacttatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttgacatacttcctctcgcatttgtttgtgacctagacagtgtagttaaactggttcaatgcattgactatgcaatacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT