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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgggcgtttctttgactttctcctcattcgagttgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTT

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 11
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|169030422|gb|FE438678.1|FE438678
EST:     CGCGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169097110|gb|FE498956.1|FE498956
EST:     CGCGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169059061|gb|FE468206.1|FE468206
EST:     CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169019958|gb|FE431023.1|FE431023
EST:     CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169064769|gb|FE473736.1|FE473736
EST:     CGCGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169028509|gb|FE439924.1|FE439924
EST:     ATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: ATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169066441|gb|FE474664.1|FE474664
EST:     CGCGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
EST: gi|169097981|gb|FE498778.1|FE498778
EST:     CGCGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAG                         GCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT
genomic: CACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCT

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), 32 (downstream exon)
Score: 18

ACAAGACATTATGAACAACACGAAGCTATGTGAAGGATATCTGACTCTCGCACGGGATCTTGATGTGATGGAGCCCAAAGTACCTGAAGATATATACAAGgtacgggcgt ... tgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgggcgtttctttgactttctcctcattcgagttgtaccacagGCTCATTTAATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTT
                     ctttgac  putative branch site (score: 18)
                           tttcttt  TA-rich tract