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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagctatgtgtttgtgtgctgtttctagcgtgtggtaatgtcatagtttgcttggtgttgtcctagGACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGAATGTGATCAGCCATCCTCAATTCACAAGCGACATCAAGTTTGCAATCG

Basic information

species Selaginella moellendorffii
transcript EFJ17647
intron # 2
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|169034317|gb|FE443090.1|FE443090
EST:     GATAGCCAAAGTTGATGGTCAGGAAGTCGGGCTCTTTGGAGTGTTTGACG                         GACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGA
genomic: GATAGCCAAAGTTGATGGTCAGGAAGTCGGGCTCTTTGGAGTGTTTGACGgtacgagcta ... gttgtcctagGACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGA
EST: gi|169035312|gb|FE442638.1|FE442638
EST:     GATAGCCAAAGTTGATGGTCAGGAAGTCGGACTCTTTGGAGTGTTTGACG                         GACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGA
genomic: GATAGCCAAAGTTGATGGTCAGGAAGTCGGGCTCTTTGGAGTGTTTGACGgtacgagcta ... gttgtcctagGACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGA

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: 35 (upstream exon), 35 (downstream exon)
Score: 190

TGCGGGCAGTGCGGGAAAAGAGCGTCGATGGAGGATTTCATTGAAGCCAGGATAGCCAAAGTTGATGGTCAGGAAGTCGGGCTCTTTGGAGTGTTTGACGgtacgagcta ... gttgtcctagGACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGAATGTGATCAGCCATCCTCAATTCACAAGCGACATCAAGTTTGCAATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgctgtttctagcgtgtggtaatgtcatagtttgcttggtgttgtcctagGACACGGAGGGCCTCGAGCTGCCGAGTTTGTAAAGAAGAACCTCTTCCAGAATGTGATCAGCCATCCTCAATTCACAAGCGACATCAAGTTTGCAATCG
                                              ttgtcct  CT-rich tract
                               atagttt  TA-rich tract