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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ22568
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM5G852502_T01 (Zea mays), 5'ss of exon 2
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagag--ccagagtttcttctttctcgggaactcaaaag----ttcgggttttccatccttgcag--------------------------------
                                                                              | ||||||||| |||||||||||||| | || ||||||||  | || ||||||| ||| || |||||||| || |||||  | || || |||||||||||||      |     |   || |||  | |   ||  | |     ||   | | | ||| |||                                    
----------------------------------------------------------------------------CAGGCATGGTGATCTGCTCAACAAGTATATGTACCTCACTGGGAGGGTGGATATGAGGCAGATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacatattctctcatccatttttttactgagtcttgacacattttttcagctcttcatgcttctcaagtgtttattttggcttgttgggagtttggtt

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 5'ss of exon 2
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaaga----gccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcag---------------------------------------
                                                                              | || |||||  | || || ||||||||||| ||  ||||| |||| || ||||| ||||||||||||||||| ||||| ||||| ||  |||||||||| |       || | |   | || ||| |       |     ||      |  | ||| |  |                                         
----------------------------------------------------------------------------CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgctttttttttttttttttttttctgtagtcaatcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 5'ss of exon 1
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaaga----gccagagtttcttctttctcgggaactcaaaagt---tcgggttttcca----tccttgcag-----------------------------
                                                                              |  | |||||  | || || ||||||||||| ||  ||||| |||| || ||||| ||||||||||||||||| ||||| ||||| ||  |||||||||| |       || | |    ||| ||| |       ||   |||   ||    | | ||    | |||| |                              
----------------------------------------------------------------------------CAGGGACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgcccttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv00s0499g00030.t01 (Vitis vinifera), 5'ss of exon 2
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagttt-cttctttctcgggaactcaaaagttcgggttttccatccttgcag-------------------------------------
                                                                            | | ||||||||  | |||||||||||||| || ||  |||||||||| || ||||||||||| |||||||| || |||||  | || || || ||||||||||    | |     | ||| |||  | | | |    |   ||      |  || ||   ||                                     
----------------------------------------------------------------------------TAGGCATGGTGACCTTCTCAACAAGTATCTTTACCTTTCTGGACGAGTAGACATGAAGCAAATTGAGAAGACAATTCAGTATCTCATAGGATCAGGAATGgtaagatcctaattcctacttatttggctgcatccactatcatcataaactatatactatgagtcttgtttcacagagaatgtaggaaaattttgccatt

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00730.t01 (Vitis vinifera), 5'ss of exon 2
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccaga-----gtttcttctttctcgggaactcaaaagttcgg----gttttccatccttgcag-----------------------------
                                                                              | || |||||  | || || ||||||||||| ||  ||||| |||| || ||||| ||||| ||||||||||||||||| |||||  |  |||||||||| |    |  |        || ||   | |        |||||   |      ||     ||  | | |                              
----------------------------------------------------------------------------CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATTGAGAAGACGATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatacac

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00740.t01 (Vitis vinifera), 5'ss of exon 3
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccaga-----gtttcttctttctcgggaactcaaaagttcgg----gttttccatccttgcag-----------------------------
                                                                              | || |||||  | || || ||||||||||| ||  ||||| |||| |||||||| ||||| |||||||| |||||||| |||||  |  |||||||||| |    |  |        || ||   | |        |||||   |      ||     ||  | | |                              
----------------------------------------------------------------------------CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGATATGAAACAAATTGAGAAGACAATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatagac

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00650.t01 (Vitis vinifera), 5'ss of exon 5
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaaga----gccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcag---------------------------------------
                                                                              | || |||||  | || || ||||||||||| ||  ||||| |||| || ||||| ||||||| ||||||||| ||||| ||||| ||  |||||||||| |       || | |    ||| ||| |       |       || |  |  | ||| |  |                                         
----------------------------------------------------------------------------CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGCGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatcccctttttttttttttttttctgtagtcag--tcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcg--ggttttccatccttgcag---------------------------------------
                                                                             || || || ||  |||| ||||||||  | ||  | || || ||||| || ||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   ||    || |   | | |||  |  | |   | |  ||                                         
----------------------------------------------------------------------------CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA