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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtgtttttgatgattgcaatgaatgaaactagattaattcctactattgcagGGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAATTAGCCTGATCGTTCGTCTTGCTGAACACGGCCTTATTCACTGTGATTTC

Basic information

species Selaginella moellendorffii
transcript EFJ10419
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|169060196|gb|FE467558.1|FE467558
EST:     GATTGGAATCGACACTGTGTTTTAATGACTCTTGTTCCAGGCTATCCTCT                         GGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAAT
genomic: GATTGGAATCGACACTGTGTTTTAATGACTCTTGTTCCAGGCTATCCTCTgtaagttgtg ... actattgcagGGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAAT
EST: gi|169054045|gb|FE462280.1|FE462280
EST:     GATTGGAATCGACACTGTGTTTTAATGACTCTTGTTCCAGGCTATCCTCT                         GGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTAGTGTTTGACACGGTAAT
genomic: GATTGGAATCGACACTGTGTTTTAATGACTCTTGTTCCAGGCTATCCTCTgtaagttgtg ... actattgcagGGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAAT

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: 23 (upstream exon), 34 (downstream exon)
Score: 4

GCTCTGCATGAACATGGATTTCCCACTCCAAAAGCAGTTGATTGGAATCGACACTGTGTTTTAATGACTCTTGTTCCAGGCTATCCTCTgtaagttgtg ... actattgcagGGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAATTAGCCTGATCGTTCGTCTTGCTGAACACGGCCTTATTCACTGTGATTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtgtttttgatgattgcaatgaatgaaactagattaattcctactattgcagGGTGCAAGTGAAAGAGCTGAAGAATCCAGCACTCGTGTTTGACACGGTAATTAGCCTGATCGTTCGTCTTGCTGAACACGGCCTTATTCACTGTGATTTC
                                  gattaat  putative branch site (score: 4)
                                        ttcctact  CT-rich tract
                            aaactagattaatt  TA-rich tract