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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggatagagatcacactttaaagttaagagctcacacaatttatttcattttttcatgcaattacag

Basic information

species Selaginella moellendorffii
transcript EFJ17214
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17214 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 12
TGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTGGTACACGA-AGCATCG-----------GTTCCAGCTTTCA--------TTCTTTCGCTCAAGgcaagtggatagagatcacactttaaagttaagagctcacacaatttatttcattttttcatgcaatta-cag
||||||||| ||||| ||||| |||||||| ||||||||||| || | || ||| |||| | || ||||| | ||| | ||| | ||| | | | ||| || | || | ||| || | | ||| | | |||| || ||||| ||| |||
TGGAGCGCTTGGAGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCAGTTGCCTTGGTGAAAGAGAGCATTGTCCCACAATTCATTCTAAATTTGAAGgtctgtttcctactcccaaagctggaattccactctctctcttacaaaagcaagtttttgacattagacatcatgattccatgcttttatcag
















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|169071789|gb|FE476646.1|FE476646
EST:     TGGCTCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCTCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
EST: gi|169019355|gb|FE427665.1|FE427665
EST:     TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
EST: gi|169063357|gb|FE472191.1|FE472191
EST:     TGGCTCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCTCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
EST: gi|169114901|gb|FE515850.1|FE515850
EST:     TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
EST: gi|169063356|gb|FE472190.1|FE472190
EST:     TGGCTCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCTCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
EST: gi|169050265|gb|FE458345.1|FE458345
EST:     TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAG                         GAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC
genomic: TGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCC

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: 31 (upstream exon), 35 (downstream exon)
Score: 11

TGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTGGTACACGAAGCATCGGTTCCAGCTTTCATTCTTTCGCTCAAGgcaagtggat ... gcaattacagGAAGGCTTCTACAACTCCCGAATCCAGAAAGGCATCGTCAAGCCCGAATCCCTGGGGCTCTACGTCTTCGCGTCCAAGCCATCCAGTGGAGCCGCCGTGA




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