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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttataacgagaaaaacgtgctattcaattgctgagttatgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG

Basic information

species Selaginella moellendorffii
transcript EFJ07343
intron # 8
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|169057927|gb|FE465525.1|FE465525
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
EST: gi|169036320|gb|FE444697.1|FE444697
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
EST: gi|169024988|gb|FE434640.1|FE434640
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
EST: gi|169039426|gb|FE447268.1|FE447268
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTG
EST: gi|169046223|gb|FE456382.1|FE456382
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
EST: gi|169115294|gb|FE517010.1|FE517010
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
EST: gi|169052748|gb|FE461165.1|FE461165
EST:     CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTG                         GCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
genomic: CAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG

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: 34 (upstream exon), 35 (downstream exon)
Score: 12

CAAGGAGCTGGAACTGACGTAGAAACAGTGAAGAAAATTCGCGATGCTATCAAAGAACAGCGCGATATCACAGTTCAGCTGCTTAACTACACAAAGAGTGgtatgttata ... atgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgttataacgagaaaaacgtgctattcaattgctgagttatgccaacagGCAAACCATTCTGGAACCTCTTCCACTTGCAGGCAATGAAAGACAACCAG
        ttataac  putative branch site (score: 12)
        atgttataa  TA-rich tract