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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgaggaaagggtcgaggaatcgatgaaatatcttgattttggcttgttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGCTCCATCCCCCGATCTCATCAATTTGTCGCGCTGGTACTCGCACATCACC

Basic information

species Selaginella moellendorffii
transcript EFJ07795
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|169054399|gb|FE462092.1|FE462092
EST:     GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGG                         CTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC
genomic: GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGGgtaagtcgag ... gttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC
EST: gi|169057097|gb|FE464660.1|FE464660
EST:     GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGG                         CTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC
genomic: GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGGgtaagtcgag ... gttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC
EST: gi|169063988|gb|FE472799.1|FE472799
EST:     GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGG                         CTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC
genomic: GGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGGgtaagtcgag ... gttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGC

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: 34 (upstream exon), 35 (downstream exon)
Score: 34

ATGGCGATCAGCTTCGACGATCTTGGTTCCAGTGCCGGGCTCAAGAGTCTCGATGAGTACCTCCTCAAGCGCAGCTACATCTCGGGgtaagtcgag ... gttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGCTCCATCCCCCGATCTCATCAATTTGTCGCGCTGGTACTCGCACATCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaggaaagggtcgaggaatcgatgaaatatcttgattttggcttgttcgcgcagCTGTCAAGCTTCCAGGGATGATCTGCTCGTCTACTTGGCTCTAGCAGGCGCTCCATCCCCCGATCTCATCAATTTGTCGCGCTGGTACTCGCACATCACC
                              tcttgat  putative branch site (score: 34)
                                          cttgttc  putative PPT
                         aaatatcttgatttt  TA-rich tract