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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagttttaacgaagtcttaaagctcgccacctttgttacatccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGACAAGGAGAAAGAGACTGGGGCGACGCGCGAGGCCGACTTGGACACAATGC

Basic information

species Selaginella moellendorffii
transcript EFJ13636
intron # 4
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|169029785|gb|FE441018.1|FE441018
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169029784|gb|FE441017.1|FE441017
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169106400|gb|FE507425.1|FE507425
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169067793|gb|FE473377.1|FE473377
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169056514|gb|FE464922.1|FE464922
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169048962|gb|FE454948.1|FE454948
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|70670001|gb|DN838578.1|DN838578
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169062830|gb|FE472866.1|FE472866
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169067792|gb|FE473376.1|FE473376
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169104371|gb|FE503733.1|FE503733
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169087508|gb|FE494625.1|FE494625
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169079757|gb|FE491166.1|FE491166
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169079758|gb|FE491167.1|FE491167
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169088324|gb|FE492042.1|FE492042
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169106399|gb|FE507424.1|FE507424
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169101312|gb|FE502507.1|FE502507
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169101313|gb|FE502508.1|FE502508
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169104372|gb|FE503734.1|FE503734
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169060085|gb|FE468695.1|FE468695
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169078349|gb|FE490382.1|FE490382
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169048961|gb|FE454947.1|FE454947
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
EST: gi|169088325|gb|FE492043.1|FE492043
EST:     GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAG                         GCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC
genomic: GCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGAC

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: 33

CGTTGCAGAGATCGTTTCAAAGGCCTACGATGTGCAAGGCAAAACCATTGGCAGTGTGGGAGCTGGAAGAATTGGGTACCATTTGCTCAAGCGTCTCAAGgtattagttt ... atccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGACAAGGAGAAAGAGACTGGGGCGACGCGCGAGGCCGACTTGGACACAATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattagttttaacgaagtcttaaagctcgccacctttgttacatccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGACAAGGAGAAAGAGACTGGGGCGACGCGCGAGGCCGACTTGGACACAATGC
         ttttaac  putative branch site (score: 33)
 ttagttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagttttaacgaagtcttaaagctcgccacctttgttacatccatgcagGCGTTCGATTGCAACCTTTTGTATTACGATCGGGTGGCCATGCCCAGTGACAAGGAGAAAGAGACTGGGGCGACGCGCGAGGCCGACTTGGACACAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA