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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgtgatcttctccaaaaatactcttgatgactatttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAATGGTTTGGCGGGTCCATTGCATGGTCTTGCAAACCAG

Basic information

species Selaginella moellendorffii
transcript EFJ29959
intron # 12
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|169033440|gb|FE441793.1|FE441793
EST:     CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTG                         GTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
genomic: CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
EST: gi|169051940|gb|FE459044.1|FE459044
EST:     CGATCACGAGGGAGGAAATGTTAGTGCACACACCGTGCGCCTG                         GTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
genomic: CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
EST: gi|169064916|gb|FE475612.1|FE475612
EST:     CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTG                         GTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
genomic: CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
EST: gi|169065764|gb|FE476213.1|FE476213
EST:     GCGATCACGAGGGAGGAAATGTTAGTGCACACACCGTGCGCCTG                         GTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
genomic: GCGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAAT
EST: gi|169059112|gb|FE468257.1|FE468257
EST:     CGATCACGAGGGAGGAAATGTTAGTGCACACACCGTGCGCCTG                         GTGGGGAGTGCACTATCGGACCCGTACCCTTTCTTT-GCGGCCGGAATGAA
genomic: CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACC-TTTCTTTTGCGGCCGGAATGAA

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), 33 (downstream exon)
Score: 31

CGATCACGAGGGAGGAAATGTTAGTGCACATACCGTGCGGCTGgtaagttttt ... ttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAATGGTTTGGCGGGTCCATTGCATGGTCTTGCAAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtttttgtgatcttctccaaaaatactcttgatgactatttatctctagGTGGGGAGTGCACTATCGGACCCGTACCTTTCTTTTGCGGCCGGAATGAATGGTTTGGCGGGTCCATTGCATGGTCTTGCAAACCAG
                                tcttgat  putative branch site (score: 31)
                                            tttatctct  putative PPT
                        aaaaatact  TA-rich tract