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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttctctttctttccctgccaattttgtcatgtttatcctaacatgctgtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCTGGTGAATCCTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ20478
intron # 7
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|169099873|gb|FE500878.1|FE500878
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169057441|gb|FE465745.1|FE465745
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169054797|gb|FE460593.1|FE460593
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169062160|gb|FE469700.1|FE469700
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169099662|gb|FE502643.1|FE502643
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169040608|gb|FE449739.1|FE449739
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
EST: gi|169050669|gb|FE457839.1|FE457839
EST:     AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAG                         ACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT
genomic: AACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCT

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: 29 (upstream exon), 35 (downstream exon)
Score: 17

GTGTTGGGGACAGACGAGCTGAATGCGTATCTGAACAAATACCACCTGGAGCTTGATGCTCACTTCGAAAGCATGGTCGGCAGgtctgttctc ... gtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCTGGTGAATCCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttctttccctgccaattttgtcatgtttatcctaacatgctgtcctcgcagACACAGCAGAAAACCCTGGTCGAAGTTCATAAACAACGACAACCAACACCTGGTGAATCCTGAG
                                 tcctaac  putative branch site (score: 17)
                                           ctgtcctc  putative PPT
                 aattttgt  TA-rich tract