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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaagatcctttttatctaccttcgccctgcggcttacatttcccttctttgtttaacttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ16666
intron # 11
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|169075245|gb|FE484114.1|FE484114
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169111211|gb|FE511371.1|FE511371
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169099806|gb|FE500811.1|FE500811
EST:     GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169075231|gb|FE484113.1|FE484113
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169100312|gb|FE501109.1|FE501109
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169100311|gb|FE501108.1|FE501108
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
EST: gi|169035258|gb|FE442610.1|FE442610
EST:     GAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCC                         GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG
genomic: GAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG

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: 19

GGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCTCCTCAACAAAGCCgtgagtaaaa ... acttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctaccttcgccctgcggcttacatttcccttctttgtttaacttccgcagGGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG
                                        gtttaac  putative branch site (score: 19)
                            tttcccttctttgttt  CT-rich tract
                                     tttgtttaa  TA-rich tract