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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatgcttctacctgtggtgctaacaatcccttacacgctttggagcag

Basic information

species Selaginella moellendorffii
transcript EFJ37593
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgta-ggtaatgcttctacctgtggtgctaacaatcccttacacgctttggagcag---------------------------------------------
||| ||||| ||  | |||||||||||||| |||||||||||||| || |||||||| || ||||||||||| ||  | || ||  | || | ||||| | |  ||| | |   | |  |    || ||      ||   |||    | |                                             
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G165631_T01 (Zea mays), 5'ss of exon 8
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatgcttctacctgtggtgct-aacaat-cccttacacgctttggagcag--------------------------
||| ||||| || || ||||| |||||||| ||||| |||||||| ||||||||||| || ||||| ||||| |  || ||||| ||  | |  |||| |   |  ||   | |||     | |||  |   | || |    |   ||  |                          
GCGAGGAGCTATTGTCACAACATTCATTGTTTGCTATGCTCTTACTTCATTCATCTCTGGATATGTCAGTGGTGCATTATACTCACGTCATGGAGgtatgggcttatttatcatgtaaaattgaactgtatacctatagttctataaggtgctcagttgttttaaatccttttggag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 9
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatgcttctacctgtggtgctaacaatccct-tacacgctttggagcag-----------------------------------------------------
 || ||||| ||||| |||||||||||||| ||||| ||||| || || ||||| || |||||||| ||||| ||| | ||||| || || |  |||| |    || |  | || || | |      ||    |    | || || ||                                                       
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGGgtaagattcgcattgatctatgctacatgttctcttgatgtttgtttaggtgcctctctctctctctctctctctctgaatgattatgactgtgcttatcattttcag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 9
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtagg---------taatgctt-ctacctgtggtgctaacaatcccttacacgctttggagcag------------------------
 || ||||| ||||| |||||||||||||| ||||| ||||| || || ||||| || |||||||| ||||| ||  | ||||| || || |  |||| |         | ||  || |||| |||     |        ||  | | || || |  |                         
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGGgtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcag

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|169044497|gb|FE451095.1|FE451095
EST:     GTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATG                         GCAAGCACTGGATCAAGTCCATGCTGCTAACGGCCTCGTTGTTTCCTTTCA
genomic: GTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatg ... tttggagcagGCAAGCACTGGATCAAGTCCATGCTGCTAACGGCCTCGTTGTTTCCTTTCA
EST: gi|169095560|gb|FE498836.1|FE498836
EST:     TTACTCGCGAAACGATG                         GCAAGCACTGGATCAAGTCCATGCTGCTAACGGGCTCGTTGTTTCCTTTCA
genomic: TTACTCGCGAAACGATGgtaggtaatg ... tttggagcagGCAAGCACTGGATCAAGTCCATGCTGCTAACGGCCTCGTTGTTTCCTTTCA
EST: gi|169088032|gb|FE492595.1|FE492595
EST:     GTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATG                         GNCA-GCACTGGATNCA-GTCCATGCTGCTAAC
genomic: GTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatg ... tttggagcagG-CAAGCACTGGAT-CAAGTCCATGCTGCTAAC

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: 23

GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgtaggtaatg ... tttggagcagGCAAGCACTGGATCAAGTCCATGCTGCTAACGGCCTCGTTGTTTCCTTTCATCTGCTTTGGCATCGGTTTTGTTCTCAACTTTGTCGCAATTTTCTATCG




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