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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcactcattcctggggattctctcagctgattccttgggattttccagCTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCGATGGTAGCAATCCCGTGTACTGGGCAAATCGGGCCTTCACGAATGTGAA

Basic information

species Selaginella moellendorffii
transcript EFJ12272
intron # 1
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|70669561|gb|DN838138.1|DN838138
EST:     TCGCGCGGAAGCGGAGCAGCTCAAGGAACAAGCCAACGCGGCATTTCAAG                         CTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCG
genomic: TCGCGCGGAAGCGGAGCAGCTCAAGGAACAAGCCAATGCGGCATTTCAAGgtaggcactc ... gattttccagCTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCG
EST: gi|169065111|gb|FE474559.1|FE474559
EST:     TCGCGCGGAAGCGGAGCAGCTCAAGGAACAAGCCAACGCGGCATTTCAAG                         CTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCG
genomic: TCGCGCGGAAGCGGAGCAGCTCAAGGAACAAGCCAATGCGGCATTTCAAGgtaggcactc ... gattttccagCTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCG

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: 20

ATGACCGACGCATCAATTCGCGCGGAAGCGGAGCAGCTCAAGGAACAAGCCAATGCGGCATTTCAAGgtaggcactc ... gattttccagCTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCGATGGTAGCAATCCCGTGTACTGGGCAAATCGGGCCTTCACGAATGTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggcactcattcctggggattctctcagctgattccttgggattttccagCTTGTAAGTTCTCCCACGCCAGGGAGTTGTACACACGGGCGATTGAGCTCGATGGTAGCAATCCCGTGTACTGGGCAAATCGGGCCTTCACGAATGTGAA
                               agctgat  putative branch site (score: 20)
                                               ttttcc  putative PPT
                                              atttt  TA-rich tract