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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgcatcacattattctgagagcattgagggcctgacgacgttttctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGAAGTGCGCATCGCGGCCGCGGGCAAGGTGACCAAGTTTTGTCGTATAATC

Basic information

species Selaginella moellendorffii
transcript EFJ15458
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|169028897|gb|FE438596.1|FE438596
EST:     GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAG                         GACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGA
genomic: GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAGgtagttgcat ... tctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGA
EST: gi|169030962|gb|FE439829.1|FE439829
EST:     GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAG                         GACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGA
genomic: GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAGgtagttgcat ... tctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGA
EST: gi|169030963|gb|FE439830.1|FE439830
EST:     GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAG                         GACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATG
genomic: GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAGgtagttgcat ... tctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATG
EST: gi|169028896|gb|FE438595.1|FE438595
EST:     GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAG                         GACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGA
genomic: GCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAGgtagttgcat ... tctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGA

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: 30 (upstream exon), 22 (downstream exon)
Score: 11

GATAAGTCCTGGCGTGTACGCTTTATGGTTGCTAATCAGCTCTACGAGCTTTGCGAAGCAGTAGGTGCGGAGGCTACGAGgtagttgcat ... tctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGAAGTGCGCATCGCGGCCGCGGGCAAGGTGACCAAGTTTTGTCGTATAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcatcacattattctgagagcattgagggcctgacgacgttttctttcaaagGACCGAACTCGTTCCAGCTTACGTGAGACTTTTGCGTGACAATGAGGCGGAAGTGCGCATCGCGGCCGCGGGCAAGGTGACCAAGTTTTGTCGTATAATC
                               gcctgac  putative branch site (score: 11)
 cgttttctttc  putative PPT
 acattatt  TA-rich tract