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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttggacag

Basic information

species Selaginella moellendorffii
transcript EFJ14096
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttggacag-----------------------
                                     |||||||| || ||||| || |||||||||||||||||  | ||||||||||| ||  | ||||||   |        | ||     | | |   |||  |  |    | || |   |                       
------------------------------------GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 17
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttggacag------------------
                                     || ||||| || ||||| |||||||| |||||||||||| ||||||| ||||| ||  | ||||||  ||        |  ||     ||       | ||||| |  |  |  ||                    
------------------------------------GGACGGTGTTAGTGAAGGTCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGGAAGgttgggtgcattttaa--tgtttttttattcttctaagctccttatagtttactaactagcgtttttttccag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 16
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttggacag-----------------------
                                     || ||||| || ||||| |||||||| |||||||||||| ||||||| ||||| ||  | ||||||  ||      |   ||    | |  | |  |||    |  | |  | ||                          
------------------------------------GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactagtgcttactttcag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA02G00510.1 (Glycine max), 5'ss of exon 17
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttg-gacag------------------------------
                                     |||||||| || ||||| ||||| ||||||||||| ||| | ||||||||||||||| | |||||  || || ||     |   | |||     | |  ||    || ||||   |||                               
------------------------------------GGATGGTGTAAGTGAAGGGCAGTTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAGgtc-agaattgattacttattcccatcataagttctagtaggtcattttataacacatgttctcacaagaatatatttatttgcag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA10G00530.1 (Glycine max), 5'ss of exon 9
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttg-gacag--------------------------
                                     |||||||| || ||||| || || ||||||||||| ||| | ||||||||||||||| | |||||  || || ||     ||    |||  | || |  |     || ||||   |||                           
------------------------------------GGATGGTGTAAGTGAAGGGCAATTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAGgtc-agaattgattactttcttccatcaaatgttctaataggtcattttataacacgtgcccacaagaatatatatttgcag

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: 26

CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTGGTCCAGAAACGGCACCACACCCGGCTATTTGCTAACGATCACGACGATA




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