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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGCAATTTATATGGCAGCAGAAGCAAGCAGTCCATTCTTTCGCTTGGGCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattattatattttataattgtatatttatttactttatttttatag

Basic information

species Selaginella moellendorffii
transcript EFJ22189
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22189 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os12g08810.1 (Oryza sativa), 5'ss of exon 4
TTTGGCAATTTATATGGCAGCAGAAGCAAGCAGTCCATTCTTTCGCTTGGGCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattattata-ttttataatt-gtatatt----tatttactttatttttatag-------------------------------------------
  | ||| |  | ||||| || |||||    || |||| |||  |  | |||||||||||||||||||| |||||||| || || || ||||| ||||||||| | ||   ||  ||||  |||| || || |    ||| |||||     |  |||                                           
GCTTGCACTGCACATGGCTGCTGAAGCCGCAAGCCCATACTTCAGGCTTGGCTATAATAGTTTGGGTGCCTTTGCAACCATCAACCACCTCCACTTTCAGgtactcttcacatggttttggaatttgtttactgttgtatctacttgtagctgttagataaatcataaatcttccagcatgcaaaattgcacgaactgtg

upper sequence: EFJ22189 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA08G43200.1 (Glycine max), 5'ss of exon 6
TTTGGCAATTTATATGGCAGCAGAAGCAAGCAGTCCATTCTTTCGCTTGGGCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgta-atattatta--tatttt---ataattgtatatttatttactttatttttatag-------------------------------------------------------------------------
  | ||| || | ||||| || ||||| || | |||||  ||| | ||||| || || || ||||||||||||||||| || || |||||||| |||||||||   ||||  |   |  |    || | || |     || | |||||| || ||                                                                           
GCTTGCACTTCAAATGGCCGCTGAAGCTAGGAATCCATATTTTAGGTTGGGTTACAACAGCTTGGGTGCATTTGCAACCATTAACCATCTCCACTTTCAGgtacgcattaccaatcaactcgagatcactgcaatgcaatattctttatgttgattattggcttgttagaatccttatctagtgttctagcagtattcaaattgacattttttgattttgacgaactcag

upper sequence: EFJ22189 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA18G10430.1 (Glycine max), 5'ss of exon 5
TTTGGCAATTTATATGGCAGCAGAAGCAAGCAGTCCATTCTTTCGCTTGGGCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaat-attatta--tatttt---ataattgtatatttatttactttatttttatag------------------------------------------------------------------
  | ||| || | |||||||  |||||||| | |||||  ||| | ||||| || || || ||||||||||||||||| || || |||||||| ||||||||| | |||| |    |  |    || | || |      | | ||| || || ||                                                                    
GCTTGCACTTCAAATGGCAGTTGAAGCAAGGAATCCATATTTTAGGTTGGGTTACAACAGCTTGGGTGCATTTGCAACCATTAACCATCTCCACTTTCAGgtactcattactgatcaactcgagatcactgcaatgcactattcttcatgttgattattggcttgtttgaattagtgttctagcagtattcaaattgacattttgtgattttgacaaacccag

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|169030374|gb|FE438656.1|FE438656
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169079376|gb|FE488068.1|FE488068
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169040656|gb|FE449787.1|FE449787
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169100821|gb|FE502203.1|FE502203
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169092902|gb|FE496340.1|FE496340
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169048387|gb|FE456309.1|FE456309
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169052621|gb|FE461688.1|FE461688
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169049338|gb|FE459796.1|FE459796
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169103760|gb|FE506125.1|FE506125
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169098310|gb|FE499627.1|FE499627
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169054361|gb|FE460806.1|FE460806
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169103759|gb|FE506124.1|FE506124
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
EST: gi|169073819|gb|FE482909.1|FE482909
EST:     GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAG                         GCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA
genomic: GCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTA

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), 26 (downstream exon)
Score: 8

TTTGGCAATTTATATGGCAGCAGAAGCAAGCAGTCCATTCTTTCGCTTGGGCTATAATAGTTTGGGTGCATTTGCAACAATAAATCATCTCCATTTTCAGgtaatattat ... atttttatagGCTTATTATTTGGGAAATTGTTTTCCTGTGGAGAAAGCTCCAACCAAATTAATACTTCACCACTATAAAGGTTTTAAAGTATATCAACTAGAAAACTATC




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