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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattgctcatgtccttttttctttgttctgggggaggtaacgctgtctttcttccttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCCGTTCGAGTGGGAATTGCTGTGGACACAGTCGGTCAGGCAGGGCGGCCCA

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 22
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|169064751|gb|FE476097.1|FE476097
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169025374|gb|FE435988.1|FE435988
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169088930|gb|FE494442.1|FE494442
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169088931|gb|FE494443.1|FE494443
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169019957|gb|FE431022.1|FE431022
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169080935|gb|FE486104.1|FE486104
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169030421|gb|FE438677.1|FE438677
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169116305|gb|FE517252.1|FE517252
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169066440|gb|FE474663.1|FE474663
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169028508|gb|FE439923.1|FE439923
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169097980|gb|FE498777.1|FE498777
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169064752|gb|FE476098.1|FE476098
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169059060|gb|FE468205.1|FE468205
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169116306|gb|FE517253.1|FE517253
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169097109|gb|FE498955.1|FE498955
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169064768|gb|FE473735.1|FE473735
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
EST: gi|169025373|gb|FE435987.1|FE435987
EST:     TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAG                         CCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC
genomic: TCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCC

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: 18

CGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAAAGCCATCATCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTAGCAATGCAGgtaaaattgc ... ttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCCGTTCGAGTGGGAATTGCTGTGGACACAGTCGGTCAGGCAGGGCGGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttttttctttgttctgggggaggtaacgctgtctttcttccttttctccagCCTAGGATGCTCATGACTGTAGACGAGAACTTAAAGCCACTGCCTGTGCCCGTTCGAGTGGGAATTGCTGTGGACACAGTCGGTCAGGCAGGGCGGCCCA
                        aggtaac  putative branch site (score: 18)
                              cgctgtctttcttcct  CT-rich tract
     tttttcttt  TA-rich tract