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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgagtagagttttgtcaatgtcttggcatacttacgtggttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCACGATGGTCCAAGGCACGAGTACAACGGAAGGTATAACTGGCGAGGAAATG

Basic information

species Selaginella moellendorffii
transcript EFJ13073
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|169087196|gb|FE496224.1|FE496224
EST:     TCCAAGGAGCAGCAG                         GCTAACAACGGGCCTAGGCCAGAGAACTTGAGGCACGAGGGTCCGAGGCAC
genomic: TCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
EST: gi|169037658|gb|FE444735.1|FE444735
EST:     CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCATTCCAAGGAGCAGCAG                         GCTAACAACGGGCCTAGGCCAGAGAACTTGAGGCACGAGGGTCCGAGGCAC
genomic: CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
EST: gi|169075280|gb|FE483538.1|FE483538
EST:     CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAG                         GCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
genomic: CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
EST: gi|169060933|gb|FE470563.1|FE470563
EST:     CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAG                         GCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
genomic: CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
EST: gi|169058679|gb|FE466888.1|FE466888
EST:     CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAG                         GCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC
genomic: CTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCAC

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: 33 (upstream exon), 35 (downstream exon)
Score: 6

TCCACTCGAGCAACCGCCAGTGGAAGGGGTGGAGCCATCGAAGTTACAACCTGCCGAAAACTCTCTGCAAGAGTCATCATCTCACTCCAAGGAGCAGCAGgtgcgagtag ... gttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCACGATGGTCCAAGGCACGAGTACAACGGAAGGTATAACTGGCGAGGAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcgagtagagttttgtcaatgtcttggcatacttacgtggttttggcagGCTAACAACGGACCTAGGCCTGAGAACTTGAGGCACGAGGGTCCGAGGCACGATGGTCCAAGGCACGAGTACAACGGAAGGTATAACTGGCGAGGAAATG
                                   tacttac  putative branch site (score: 6)
                                      atactta  TA-rich tract