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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcaagctttttcatttcgaactgtcttctaacgttgctgtgtctctcgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCAGGGAAAACGTTGCAAGTCATTTACAG

Basic information

species Selaginella moellendorffii
transcript EFJ23410
intron # 3
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|169097662|gb|FE497428.1|FE497428
EST:     GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATA                         AGGCCGTTCCTAAAAAGATCTTGGAGCTTATGGACGTTCCTGGCCTTACCA
genomic: GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATAgtaagctcaa ... cgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCA
EST: gi|169087626|gb|FE494665.1|FE494665
EST:     GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATA                         AGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCA
genomic: GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATAgtaagctcaa ... cgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCA
EST: gi|169094287|gb|FE492133.1|FE492133
EST:     GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATA                         AGGCCGTTCCTAAAAAGATCTTGGAGCTTATGGACGTTCCTGGCCTTACCA
genomic: GGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATAgtaagctcaa ... cgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCA

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: 26 (upstream exon), 32 (downstream exon)
Score: 5

GATAGCGAAGACCCTTCGTCTTTGAAGAAACCACGGGTTGTTTGGTCAGTGGAGCTTCACCAGCAGTTCGTGAACGCTGTCAACAAGCTCAACATTGATAgtaagctcaa ... cgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCAGGGAAAACGTTGCAAGTCATTTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctttttcatttcgaactgtcttctaacgttgctgtgtctctcgtttcgcagAGGCCGTGCCTAAAAAGATCTTGGAGCTTATGGATGTTCCTGGCCTTACCAGGGAAAACGTTGCAAGTCATTTACAG
                        ttctaac  putative branch site (score: 5)
                                        tctctcgtttc  putative PPT
     tttttcattt  TA-rich tract