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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcaaaacttcgtttcatgcgcttaccgacttgcatgcatggattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACCTACGAGGATCTCATGGCGGCAGGAATTATCGATCCCACAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ16507
intron # 11
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|169030583|gb|FE439541.1|FE439541
EST:     AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAG                         GTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
genomic: AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
EST: gi|169072619|gb|FE481584.1|FE481584
EST:     AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGTGTGGTCGTCGAAAAG                         GTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACGGGAACC
genomic: AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
EST: gi|169088884|gb|FE494422.1|FE494422
EST:     AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAG                         GTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
genomic: AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
EST: gi|169082801|gb|FE486256.1|FE486256
EST:     AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGTGTGGTCGTCGAAAAG                         GTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACGGGAACC
genomic: AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
EST: gi|169076090|gb|FE484392.1|FE484392
EST:     AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAG                         GTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC
genomic: AACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACC

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), 34 (downstream exon)
Score: 27

ATTGGCGCAGACATTGTCAAGCGCGCCTTGGGCTACCCGATCAAACTCATCGCCAAGAATGCAGGAGTGAACGGGAGCGTGGTCGTCGAAAAGgttggcaaaa ... gattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACCTACGAGGATCTCATGGCGGCAGGAATTATCGATCCCACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggcaaaacttcgtttcatgcgcttaccgacttgcatgcatggattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACCTACGAGGATCTCATGGCGGCAGGAATTATCGATCCCACAAAG
                       cgcttac  putative branch site (score: 27)
                                               ttttcc  putative PPT
       aaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcaaaacttcgtttcatgcgcttaccgacttgcatgcatggattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACAGGAACCTACGAGGATCTCATGGCGGCAGGAATTATCGATCCCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT