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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctgctactcggctcgcttgtttcttttacgtttcggactccatgccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAGGACCCCCGTTTTCGCCAGGTTCTCGAGCGTGGCGGCCGAGCGTGGATTC

Basic information

species Selaginella moellendorffii
transcript EFJ21541
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|169086911|gb|FE495120.1|FE495120
EST:     TTCGTCCATGCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169097972|gb|FE498769.1|FE498769
EST:     TTCGTCCATGCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169041617|gb|FE449045.1|FE449045
EST:     TTCGTCCATGCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169095390|gb|FE497496.1|FE497496
EST:     TTCGTCCATGCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169018437|gb|FE427246.1|FE427246
EST:     TTCGTCCATGCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169069871|gb|FE477536.1|FE477536
EST:     GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169061633|gb|FE469420.1|FE469420
EST:     GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG
EST: gi|169052855|gb|FE461220.1|FE461220
EST:     GCCAAAGGTGCCGGAGCTCATGGATACTTCGAAGTTACAAA                         GGACGTATCAAACTTGTGCAAGGCAAAGTTCTTGAGCGAGCCCGGAAAGAG
genomic: GCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAG

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: 33 (upstream exon), 28 (downstream exon)
Score: 5

ATTTGTTTGAGAAGCAAGCACGGCTCAACCGTGAGAGAGTTCCCGAGCGCGTCGTCCATGCCAAAGGTGCCGGAGCTCACGGATACTTCGAAGTTACAAAgtaagtctgc ... ccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAGGACCCCCGTTTTCGCCAGGTTCTCGAGCGTGGCGGCCGAGCGTGGATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctactcggctcgcttgtttcttttacgtttcggactccatgccatttgtagGGACGTATCAAACTTGTGCAAGGCCAAGTTCTTGAGCGAGCCCGGAAAGAGGACCCCCGTTTTCGCCAGGTTCTCGAGCGTGGCGGCCGAGCGTGGATTC
                    tttctttta  TA-rich tract