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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacgactaaaagttctattcgattcgtcttgcgaactaatgccgattttttcttgcgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG

Basic information

species Selaginella moellendorffii
transcript EFJ06373
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06373 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: PP1S113_110V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------gtagacgactaaaagttctat---tcgattcgtcttgcgaactaatgcc-----gattttttcttg--cgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG
                            |   ||   ||| ||| | |   | | || || ||    ||     ||     ||   ||   ||   | ||||||| ||||| || ||||||   ||||||||    ||  | |  |||||||| |||||||||||||| |||||||||||||| 
attcatatattttcgaaggattttggtattcccggagaaaggttttttgtatggctttgttttctctaccttcaccacatagacacttctgtgattgcagGATTCTGGATGCCCATGCTTTAAAGGAGGTCCTCGTACAGTGCAAAATTTGAGGAAGCGTTTCCATCTAAGCTTGACTGAGGAA
















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|169034965|gb|FE445866.1|FE445866
EST:     CGTGTCGGAAGCACGCAGAACGGATAATTCTTCTGGTGGAAATGATGCAG                         GATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTG
genomic: CGTGTCGGAAGCACGCAGAACGGATAATTCTTCTGGTGGAAATGATGCAGgtagacgact ... tcttgcgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaaagttctattcgattcgtcttgcgaactaatgccgattttttcttgcgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG
                            aactaat  putative branch site (score: 2)
                                        ttttttcttgc  putative PPT
                                       attttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacgactaaaagttctattcgattcgtcttgcgaactaatgccgattttttcttgcgtagGATTCGGGATGTCCTTGCTTTCGTGGAGGTCCCAAAACGATCCTGAATTTGAGAAAGCGTTTCCATCTTAGCTTGACTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG