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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgttttttggaaagtctaaaacgatgtggctaagctctttctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG

Basic information

species Selaginella moellendorffii
transcript EFJ29683
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29683 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G09200.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtaagcgttttttggaaagtc-taaaacgatgtggc-taagctctttctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG
                                            ||    ||   | | |  ||  |      || ||   ||   |   ||  ||||||||  ||||||| || ||||||||||| |||||||| || || ||||| |||||||| || || || || || ||| | ||   |  |||||| ||  |||
tcaggcctcaacttcaaatactggaaggccaagtttactgttttgtgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG
















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|169062428|gb|FE469487.1|FE469487
EST:     AGTGGAAGAAGCGCGACATCACAGGAATCTACCACAAGTGGCAAACGATG                         AACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATC
genomic: AGTGGAAGAAGCGCGACATCACAGGAATCTACCACAAGTGGCAAACGATGgtaagcgttt ... tctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATC
EST: gi|169030597|gb|FE437904.1|FE437904
EST:     AGTGGAAGAAGCGCGACATCACAGGAATCTACCACAAGTGGCAAACGATG                         AACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATC
genomic: AGTGGAAGAAGCGCGACATCACAGGAATCTACCACAAGTGGCAAACGATGgtaagcgttt ... tctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATC

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: 32 (upstream exon), 21 (downstream exon)
Score: 4

TCCAAACGCGTGTGGCTGGGCCTACGGGATGAACATCTTCGACCTGGAGGAGTGGAAGAAGCGCGACATCACAGGAATCTACCACAAGTGGCAAACGATGgtaagcgttt ... tctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcgttttttggaaagtctaaaacgatgtggctaagctctttctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG
                   gtctaaa  putative branch site (score: 4)
                                        ctctttctcttgc  putative PPT
        tttttt  TA-rich tract