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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctctatatcccgattatatatgttttggacaatggaaagccgatagatgttttgatcgtctttgtgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCCAA

Basic information

species Selaginella moellendorffii
transcript EFJ16229
intron # 2
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|169058925|gb|FE468746.1|FE468746
EST:     GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAG                         GTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
genomic: GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAGgttagtctct ... tgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
EST: gi|169030430|gb|FE439492.1|FE439492
EST:     GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAG                         GTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
genomic: GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAGgttagtctct ... tgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
EST: gi|169078808|gb|FE489632.1|FE489632
EST:     GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAG                         GTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
genomic: GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAGgttagtctct ... tgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
EST: gi|169078032|gb|FE489883.1|FE489883
EST:     GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAG                         GTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC
genomic: GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAGgttagtctct ... tgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCC

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: 67

GTTGTGGAAGGCTGTGATGAAACTGGGAGGATACGAACAGgttagtctct ... tgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttggacaatggaaagccgatagatgttttgatcgtctttgtgtttaccagGTGACCTCTGGAAAGCTTTGGCGTCAAGTCGGCGATTCCTTCAAACCCCCCAA
                              ttttgat  putative branch site (score: 67)
                                       tctttgt  putative PPT
                           atgtttt  TA-rich tract