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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcgttcttttggcatgttttcttcactatcctaccttgacattttggacttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ23966
intron # 4
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|169025475|gb|FE434945.1|FE434945
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169021382|gb|FE431173.1|FE431173
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCGTGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169080275|gb|FE488915.1|FE488915
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCGTGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169030649|gb|FE438749.1|FE438749
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCGTGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169055950|gb|FE466152.1|FE466152
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169044562|gb|FE450614.1|FE450614
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
EST: gi|169066556|gb|FE476287.1|FE476287
EST:     TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACAC                         ACCGTGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
genomic: TTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG

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: 32 (upstream exon), 35 (downstream exon)
Score: 13

GCTGGGTGGACTTCGTCGGCAACATGCCTATGAAGATATGCTATCCGGCTTTGCAGGGAGAGGAGTGGCGTATCATCACCGGAAGTGATCCCAAAAACACgtaagctcgt ... ttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttggcatgttttcttcactatcctaccttgacattttggacttggagacagACCATGGTCGTATCACAACGGAGGTTCCTGGCCGACTCTCTTGTGGCAG
                             ccttgac  putative branch site (score: 13)
 atgtttt  TA-rich tract