Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGCAGCTCTGGCTGGGAGGCTTGGTTTCCAAAGGCAGCAAAGTGTTGGTCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaattctttctatccaatcgaggattccagagagaactttgtttccag

Basic information

species Selaginella moellendorffii
transcript EFJ11187
intron # 6
splice site 5'
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|169035103|gb|FE444899.1|FE444899
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169024425|gb|FE434363.1|FE434363
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169070383|gb|FE479348.1|FE479348
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169111354|gb|FE510903.1|FE510903
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169057337|gb|FE466798.1|FE466798
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169103452|gb|FE507572.1|FE507572
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169064647|gb|FE471378.1|FE471378
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169024411|gb|FE434362.1|FE434362
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169099416|gb|FE501006.1|FE501006
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169024773|gb|FE433307.1|FE433307
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169064646|gb|FE471377.1|FE471377
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169048832|gb|FE455299.1|FE455299
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169038579|gb|FE446904.1|FE446904
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169069403|gb|FE479486.1|FE479486
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169059196|gb|FE467198.1|FE467198
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTGAGAGGAGGCCCCCAGATGCTGCAGCTCAGCCTCGACGGC
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGC
EST: gi|169038580|gb|FE446905.1|FE446905
EST:     TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAG                         GGGAAGAAACTG
genomic: TCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 109

CGGGCAGCTCTGGCTGGGAGGCTTGGTTTCCAAAGGCAGCAAAGTGTTGGTCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaa ... ttgtttccagGGGAAGAAACTGAGAGGAGGCCCCCAAATGCTGCAGCTCAGCCTCGACGGCAAGCGTCTCTACGTGACAAACTCGCTGTTCAGCTCCTGGGACAATCAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGCAGCTCTGGCTGGGAGGCTTGGTTTCCAAAGGCAGCAAAGTGTTGGTCGAGAGCTCTACCGGAGAAGACTGGCAATCCAGCGTTCCTCCAGTCCAGgtaagcgaaattctttctatccaatcgaggattccagagagaactttgtttccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA