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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctggaatttatctgtgctgaagtttaatgactaacacattctgccagGCTGCGATGCCCTCTCTTGTGCG

Basic information

species Selaginella moellendorffii
transcript EFJ14843
intron # 6
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|169062984|gb|FE472942.1|FE472942
EST:     GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATG                         GCTGCGATGCCCTCTCTTGTGCG
genomic: GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATGgtatgctgga ... attctgccagGCTGCGATGCCCTCTCTTGTGCG
EST: gi|169054410|gb|FE462103.1|FE462103
EST:     GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATG                         GCTGCGATGCCCTCTCTTGTGCG
genomic: GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATGgtatgctgga ... attctgccagGCTGCGATGCCCTCTCTTGTGCG
EST: gi|169020526|gb|FE429797.1|FE429797
EST:     GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATG                         GCTGCGATGCCCTCTCTTGTGCG
genomic: GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATGgtatgctgga ... attctgccagGCTGCGATGCCCTCTCTTGTGCG
EST: gi|169105270|gb|FE506372.1|FE506372
EST:     GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATG                         GCTGCGATGCCCTCTCTTGTGCG
genomic: GGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATGgtatgctgga ... attctgccagGCTGCGATGCCCTCTCTTGTGCG

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), 23 (downstream exon)
Score: 10

ACGTTTGATGCGGTAGACGGTAAACAGGCGAGGCGAACCAATTCTTCCAGTCCTCTTGGAGAATTGTTTGACCATGgtatgctgga ... attctgccagGCTGCGATGCCCTCTCTTGTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgctggaatttatctgtgctgaagtttaatgactaacacattctgccagGCTGCGATGCCCTCTCTTGTGCG
                                    gactaac  putative branch site (score: 10)
                                              ttctgcc  putative PPT
            aatttatct  TA-rich tract