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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagctgcactccactcgcctagtgcatcatacttaatttttcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGCTTCTTCTTAAAGCGCGCCCGGCTAGAAGGTCCATGTCCGACTTTGCCAA

Basic information

species Selaginella moellendorffii
transcript EFJ23755
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|169048892|gb|FE456035.1|FE456035
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169036630|gb|FE446554.1|FE446554
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169048891|gb|FE456034.1|FE456034
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169103281|gb|FE507310.1|FE507310
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169110117|gb|FE513358.1|FE513358
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169103282|gb|FE507311.1|FE507311
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
EST: gi|169110116|gb|FE513357.1|FE513357
EST:     ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAG                         TGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC
genomic: ATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGC

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: 30 (upstream exon), 30 (downstream exon)
Score: 26

AGTCAAGAAAACAGGCTTAAAAAAGCCATGTCTATGGACAACTCCCCAAGATCACCTCTTCAGGAACCTATCAGAACCCAAAGCTACGACAGAGTGCAAGgtaagagctg ... tcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGCTTCTTCTTAAAGCGCGCCCGGCTAGAAGGTCCATGTCCGACTTTGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagagctgcactccactcgcctagtgcatcatacttaatttttcacttccagTGGAGGATGATATGCAATCTTCTAGCGTGGAAGATGCCAGGAGGCGAATGCTTCTTCTTAAAGCGCGCCCGGCTAGAAGGTCCATGTCCGACTTTGCCAA
                                   acttaat  putative branch site (score: 26)
                                         tttttcacttcc  CT-rich tract
                              atcatacttaattttt  TA-rich tract