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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagccctggcctttgtagctttgctcatacgacgagattatgttacag

Basic information

species Selaginella moellendorffii
transcript EFJ14096
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagccctggcctttgtagctttgctcatacgacgagattat-gttacag-----------------------------------------
| ||||| || ||||| ||||| ||||| ||| | |||||||| |||||||| || |||||||| || |||||||||||   || |        | ||||||    ||  ||||    ||  || | |||||                                           
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctga-catatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G045821_T01 (Zea mays), 5'ss of exon 11
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgt-aagttgatggagccctggcctttgtagctttgctcatacgacgagattatgttacag
||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||   |||     | |||    ||   |  | ||  |  |   || |             
GCACTGTGGTGGACTCGAAGATCTGCCATCCAACTGAGTTTGATTTCTACCTGTGCAGCCATGCTGGCATTCAGgttgggtttccctatcccatagctgaatctcattaattgttttaccaag-----------

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 19
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagt-tgatggagccctg------gcctttgtagctttgctcatacgacgagattatgttacag-----------------------------------
| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||| || || |||||||   | |||  |   ||       ||  | |  |||||  || |    || ||||  |   ||                                   
GAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaaaagtaatgtggatttgtggaagaccgatattactttgtgca-atcctgacattacatgttagctggaatattctaccgtacctgtcatttgtgagtg

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA17G12850.1 (Glycine max), 5'ss of exon 19
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgat-ggagccctggcctttgtagctttgctcatacgacgagattatgttacag----------------------------------------
| |||||||||||||| ||||| || ||||| ||||| || ||||||||  | ||||| ||||| || ||||||||| | | ||   ||  ||    |   |    |    | ||      |||| |||| | |                                        
GTACTGTGGTGGATTCTAAGATCTGTCATCCTACGGAATTCGACTTCTATTTATGCAGTCATGCGGGAATTCAGgtatgataattacagtactcctataatttatctacggcttaaacttcgattttgttcctgtacaaaatttatttacaccccatttgtatgtataaaaggg

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 19
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgta------agttgatggagccctggcctttgtagctttgctcata-cgacg-agattatgttacag-------------------------
| ||||| || ||  | || || || |||||||| || || |||||||||||||| |||||||| || |||||||||      |  |   | |      |    | |  | ||   | || | |   |||| |  | |||                          
GTACTGTAGTTGACACTAAAATATGTCATCCAACTGAATTCGACTTCTACCTTTGTAGCCATGCGGGTATTCAGgtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 19
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagcc-ctggcctttgta-gctttg---ctcatacgacgagattatgttacag-------------------------------------------------------------------------------------------------------------------
| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||| || || ||||||  ||| || |  |  |     ||| | |   ||    | |||  |    |  |    ||||                                                                                                                   
GTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAGgtaccttgttgaactcattaaatattgcaaggcctgaaatttataatagataagaaaaacacagaagttctcaatttctgcaagagaactttcaagttggtgttggcatgccaggatggttttgaatgtaaagtactacatgtcaagaatttgtttgtactgaaattgacatttggcag

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 5'ss of exon 17
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagccctggcctttgtagctttg-ctcatacgacgagattatgttacag----------------------------------------
|||| ||||| ||||| || ||||||||||| || || ||||| || || || ||||||||||| || ||||||||||     ||     ||  | || | |  ||   || |   ||    |  ||  |  ||                                        
GCACAGTGGTTGATTCTAAAATTTGCCATCCGACTGAATTTGATTTTTATCTCTGCAGCCATGCTGGTATTCAGgtaaagctctgtttttctttcattggaatattaaactgactagatttaaaaataatgaagtgtgtttcttctaaagtgatgaaaagcaacatattgccca

upper sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 5'ss of exon 16
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagccctggcctttgtagctttgc--------tcatacgacgagattatgttacag-----------------------------------
| ||||| ||||| ||||||||||| || || |||||||||||||| || |||||||| ||||| || ||||||||   |  ||  |       | ||| | | ||||         ||||  |     | | ||  |                                      
GGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAGgttcat--atccattttatacttttattgatttgtgaaatgtttcatctgctagaaatgtggaagcatatgtatctttgtaaggaatagaatttctgatcgc

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), 34 (downstream exon)
Score: 75

GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG




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