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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaagctgtttttaggaagtcgtcgattgtaagctctctttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGCCTATGGGACGTGGTCACGAATCAG

Basic information

species Selaginella moellendorffii
transcript EFJ17647
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|169034317|gb|FE443090.1|FE443090
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGNAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169035885|gb|FE442353.1|FE442353
EST:     TGGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCTTTCCAGAGATAAAG                         GGGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169116395|gb|FE517758.1|FE517758
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169035312|gb|FE442638.1|FE442638
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGG
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169102661|gb|FE503947.1|FE503947
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169116396|gb|FE517759.1|FE517759
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
EST: gi|169034316|gb|FE443089.1|FE443089
EST:     TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAG                         GAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC
genomic: TTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGC

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: 35 (upstream exon), 34 (downstream exon)
Score: 69

GCACCTGGCGTGTGGGAGGCGTCCTGGCAGTTTCACGAGCGTTTGGAGACAGGCTCTTGAAGCAATTCGTTGTTGCCATTCCAGAGATAAAGgttcgaagct ... tttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGCCTATGGGACGTGGTCACGAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgaagctgtttttaggaagtcgtcgattgtaagctctctttattttagGAGGAGGTGATAACGGAAGATGTGGAGTTTTTCGTGATCGCCAGCGACGGCCTATGGGACGTGGTCACGAATCAG
                                           ctctctttatttt  CT-rich tract
                                           tctttatttta  TA-rich tract