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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ19598
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaa---aaatttgcact-ttgcag-----------
 || || ||||| || ||||||||||||||||| || || |||||||| || |||||||| ||  ||||||| || ||||| ||||| || || || ||   |  |||| ||    |     |  |  | | || | |  || |   ||    | ||   ||| ||  |            
GTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGgtttgtccatcaaaataattttaggctttagtgttatgttttagtaaaaccagaagttgatttcctactgttttaactactgtccag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os11g37890.2 (Oryza sativa), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctct------tttgtggggaatctgaaaaaatttgcact--ttgcag--------------
 || |||||||| || ||||| || || ||||| || |||||||||||||| |||   || || ||||||||||||||||| ||||| ||||| || |  |||       |   | | |   |   |  |       | |||     ||    | |||   |||||  || |||              
GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttctaaactttcccactgatatatgttctgttgcaaattgatatgttaattattgttacaaaacagcactgatttcagtaattaccttttag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactttgcag--------------
 || || ||||| || ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||| || ||||| ||||| || || || ||   |   ||| | ||  |     | ||  |  || |      ||      |||| |  |       |              
GTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAGgtgtgttcatcgaaatacaatgacg--ttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgt------atgaa-----aaagaaaaaaaaaaaaaaaacttcttctcttttgtgg-ggaatctgaaaaaatttgc---actttgcag----------
 ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| |||||||||||||| || ||       |||       ||      ||   |      |||||   |||      || ||  | |  ||||||    | ||||             
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttc--ttctcttttgtggggaatctgaaaaaatttgcactttgcag----------------------------
 ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || || |||||     ||       ||  |    |||   |   | | ||     |  | |||| | ||   ||  ||||                            
GTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggcta-gcagggatatatttaatttttgacttttatag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactt-tgcag------
 || |||||||| || ||||| || || || || |||||||||||| |||||||||   | ||||| ||||||||||||||||| ||||| ||||| || ||  |    |      | |      | ||     ||| || |   | |   |     ||   |  ||| |      
GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttgtgatt--attttttatatgttcttgctaaagatttatgagtcttttcttatgtgatgttttgatgctgatatag

upper sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 5'ss of exon 3
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgt------atgaaaaagaaaaaaaaaaaaaaaacttctt------ctcttttgtggggaatctgaaaaaatttgcacttt-gcag---------
 || || ||||| || ||||| ||||| ||||| || ||||||||| |||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||       |   || |   | |||      | || |||       |  |||||     || || || |||||    ||| ||           
GTTCTTCTATGCCTCTAGTGCTTGCATCTACCCTGAATTTAAGCAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCATGGCCTGCAGAGgttagttagttttaatgctcagaaatgtggcatctgcttgaattttttatttgtaaattatttggaagaatttatttttttgcttgttttttag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactttgcag

- - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG