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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttcccagtttgtcgatcagtagcaaagagcttttctcgtttctttcctttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCCGACCGTCATCTCGTCGAGTCTGTCGTCGACTCCGCGAAAGACGAGTACA

Basic information

species Selaginella moellendorffii
transcript EFJ17636
intron # 3
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|169055128|gb|FE461028.1|FE461028
EST:     CAAACAACCAAGGAGCTTATAAGCAGCTTCTCAAAGACCTCATCGTCCAG                         GCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC
genomic: CAAACAACCAAGGAGCTTATAAGCAGCTTCTCAAAGACCTCATCGTCCAGgtaagtcttc ... ttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC
EST: gi|169101756|gb|FE501248.1|FE501248
EST:     CAAACAACCAAGGAGCTTATAAGCAGCTTCTCAAAGACCTCATCGTCCAG                         GCCTTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC
genomic: CAAACAACCAAGGAGCTTATAAGCAGCTTCTCAAAGACCTCATCGTCCAGgtaagtcttc ... ttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC
EST: gi|169055127|gb|FE461027.1|FE461027
EST:     AACAACCAAGGAGNCTTATAANGCAGCTTCTCAAAGACCTCATCGTCCAG                         GCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC
genomic: AACAACCAAGGAG-CTTATAA-GCAGCTTCTCAAAGACCTCATCGTCCAGgtaagtcttc ... ttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCC

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: 32 (upstream exon), 34 (downstream exon)
Score: 19

TCTCGTCCGTGAGATGAAGGACGCTGCCATGAAGCAGCTCCAAAACACATCAAACAACCAAGGAGCTTATAAGCAGCTTCTCAAAGACCTCATCGTCCAGgtaagtcttc ... ttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCCGACCGTCATCTCGTCGAGTCTGTCGTCGACTCCGCGAAAGACGAGTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtttgtcgatcagtagcaaagagcttttctcgtttctttcctttcaactcagGCCCTGATAAGATTGAAGGAGCCTGCCGTGCAAATTCGCTGCCGAGAATCCGACCGTCATCTCGTCGAGTCTGTCGTCGACTCCGCGAAAGACGAGTACA
                          cttttctcgtttcttt  CT-rich tract
                                   tttcttt  TA-rich tract