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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccaggtagctaattacgtgctggtggaagcttttcttttctctgacactgccagccgcgtttgcatatccagATGACTCGGTGGAGTTAACGCACGAGACAGTGGCATCTTGGCTGTTCAAGGGCCAGACATACTACAAGTACGCGGTGAATGCCACCAATGCATCCAAGCA

Basic information

species Selaginella moellendorffii
transcript EFJ12750
intron # 8
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|169101776|gb|FE500748.1|FE500748
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169101776|gb|FE500748.1|FE500748
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169101776|gb|FE500748.1|FE500748
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034314|gb|FE443087.1|FE443087
EST:     CACAACCCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034314|gb|FE443087.1|FE443087
EST:     CACAACCCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034314|gb|FE443087.1|FE443087
EST:     CACAACCCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034315|gb|FE443088.1|FE443088
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034315|gb|FE443088.1|FE443088
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc
EST: gi|169034315|gb|FE443088.1|FE443088
EST:     CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCGTCC                      
genomic: CACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAA---G-CCgtccaggtag ... gcatatc

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), 15 (downstream exon)
Score: 9

CTCCACGGCGGCTACTACAACTCCCGCGACGACTCCGGATCCGACTTGAACACAAACCCAGTGGAGGCATTGCCGCTGCCTCCAACCAGTGCTGCAAGCCgtccaggtag ... gcatatccagATGACTCGGTGGAGTTAACGCACGAGACAGTGGCATCTTGGCTGTTCAAGGGCCAGACATACTACAAGTACGCGGTGAATGCCACCAATGCATCCAAGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggtggaagcttttcttttctctgacactgccagccgcgtttgcatatccagATGACTCGGTGGAGTTAACGCACGAGACAGTGGCATCTTGGCTGTTCAAGGGCCAGACATACTACAAGTACGCGGTGAATGCCACCAATGCATCCAAGCA
                      ctctgac  putative branch site (score: 9)
             ttttctttt  TA-rich tract