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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttctctcctccacttctcgtaactccgttttaaaaactttggaaagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG

Basic information

species Selaginella moellendorffii
transcript EFJ07601
intron # 5
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|169066302|gb|FE472978.1|FE472978
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169066303|gb|FE472979.1|FE472979
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169067004|gb|FE475981.1|FE475981
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169044683|gb|FE452477.1|FE452477
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169058558|gb|FE464284.1|FE464284
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169094622|gb|FE494548.1|FE494548
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169094623|gb|FE494549.1|FE494549
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169067005|gb|FE475982.1|FE475982
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169044684|gb|FE452478.1|FE452478
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
EST: gi|169058559|gb|FE464285.1|FE464285
EST:     GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG                         GTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
genomic: GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG

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: 13 (upstream exon), 34 (downstream exon)
Score: 6

GATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAGgtctgtttct ... aagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctctcctccacttctcgtaactccgttttaaaaactttggaaagagaacagGTTTTCGATACCAAGTTTGCTAGAATTGGTGTGG
                  tcgtaac  putative branch site (score: 6)
                             ttttaaaaacttt  TA-rich tract