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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag

Basic information

species Selaginella moellendorffii
transcript EFJ14701
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g26720.1 (Oryza sativa), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag----------------------------
|    |||  | | | |||||||||||||||| || |||||||| ||||| || || || |||||||||||| |||||||| |    |||| | |       |   | |     ||||   ||  |     | | |         || |                              
GAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAGgta-attaattaacacaaaacagaaccactgcaaccgcataatcagtgcccgaaacaggggaagcagcacctactcctaaccttcaatatccatcaaaatt

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g58350.1 (Oryza sativa), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgca--tggacacagtatc--tatctgc--atcgctgtcaacag----------
|     ||  |  |  ||||||||||||| || || |||||||| |||||||| |  ||||| ||||||| |||||||||   |  || |   | |   |     ||  |   || |  ||||    |||     | |||   || |   |  |  |          
GATCGGAATGTGCATATGATCATCACGGATTACTGCATGCCGGAGATGACAGGGTTCGATCTCCTCAAGAGGGTCAAGgttagcatttcagacagtcactcagctcctctctctgtatctggatgttgtagtagcaactgaagattggattggattgtgcatggcag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os01g72330.1 (Oryza sativa), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctt-----taataaattg----tttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag-----------------------------------------
|  ||| |  | ||| |||| ||||| ||||| || ||||| |  |||||||| |||||||||||||||| ||| ||||||     ||      |   |||||     ||     | |   || |||  |    |  ||  | ||  | ||||  |   |                                         
GAGATTGATGTCAACCTGATAATCACTGACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAGgtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttg--ttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os04g44280.1 (Oryza sativa), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacac----gctttaataa--attgtttgatgccagtt-------gatgcatggacacagtatctatctgcatcgctg--tcaacag-----------------------
|     ||  | | | |||| ||||| ||||| || |||||||| ||||| || ||||| || || |||||||||||||||  |    | | | |  |   || ||||   | | ||         | |  |  || | ||    ||  | |  |||  |  |||                        
GAACCGAATGTGAGCATGATTATCACTGACTACTGGATGCCGGAGATGACCGGGTATGAACTCCTGAAGAAGGTCAAGgtaatccggtgatatcaccaccgttatttgggccaacttccatagtactcctcgtgcatattactactcaccttttctgatttgacaatagaaaatggcatatctttgcag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G148056_T01 (Zea mays), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatc-tgcatcgctgtcaacag-------------------------
|     ||  | | | |||||||||| ||||| || ||||| || ||||| ||||| || |||||||| |||||||||||| |      | ||  ||   ||   || |  |   | |  || ||     | ||  || |  |     | |                          
GAGCCGAATGTGAGCATGATCATCACAGACTACTGGATGCCAGAGATGACCGGCTACGACCTGCTCAAAAAGGTCAAGgta-attaaccattagcttcgatggcacctgcagcctc-tcaactcaactgttgtcgcgcgtaacatctgatacagcctgcttccgccctactaagcag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
------------------GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattg-tttgatgccag---ttgatgcatgg-acacagtatctatctgcatcgctgtcaacag------------------------------------------
                  |   |     | ||| |||||||||| ||||| || ||||| |  |||||||| ||||| |||||||||||| |||||||     ||  | ||    |   ||||  | |    |  || || |  |    | |||  |   ||| |||   | |                                           
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA04G29250.1 (Glycine max), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgt---ttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag-------------------------
|   |  || ||||| ||||||| || || || |||||||| ||||||||||||||||||||||| || ||| |||||||| || | |     | || |    ||||| ||     ||  | |      ||    ||   || | |||  | |                          
GATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACAGGCTATGATCTGCTGAAAAAGATCAAGgtaaactcctgggatatttttatactgatggcatggcttgtgtagttgtgttactcttccttat-gttgtttatactttataaaaatagtttactattttc

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA11G21650.1 (Glycine max), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatctg-catcgctgt-caacag-------------------------------
|   |  || ||||| ||||||| || || || |||||||| |||||||| |||||||||||||| |  ||| ||||||||||      || || |  || |||     | || | ||  |  | |  | | | |  | ||  | |   |  |                               
GATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAGgtaca------aaaaactccttggatatttttagacggataaaagccgcctgtgtttctcttctttatgtgattgatctagtttatatttcaaaaaaatatttcac

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv13s0067g03070.t01 (Vitis vinifera), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag----------------------------------
|     ||  | || ||||| || || ||||| |||||||| | ||||||||||||||| ||||||||||  ||||||||        | | |  ||    ||          ||| |  || |  | | ||    | |   | |  |                                     
GTTTCAAAGGTGAATTTGATAATTACAGACTACTGTATGCCAGGAATGACAGGCTATGAGCTGCTCAAGAGAGTCAAGgttagtaaagtcaaattttccaggaaagttccctctgctttaac-ctttttttaagcccttaattctttatttttatacttttctttttttctctccttccaagcag

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv17s0000g07580.t01 (Vitis vinifera), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgt-----acacgc--tttaataaattgtttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag----------------------
|   | ||  | ||  ||||||| |||||||||| |||||| |  |||||||| |||||  ||||||||||| |||||||     |   ||  ||| ||||||||  |  ||   ||   ||| |||   | |     | |             |||                       
GGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAGgtttgatatttgccgtttgataaattgcctcttgtgggtc--tgcttggttgctgggaaaacccatgaaaggaaatacaatctggttcctccattttatggt

upper sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv13s0067g03460.t01 (Vitis vinifera), 5'ss of exon 3
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgc-tttaataaattgtttgatgccagt---tgatgcatggacacagtatctatctgcatcgct-gtcaacag----------------------------
|  |  ||| |||| || || || ||  | |||| |||||| | |||||||||||||||||| ||||| ||| ||||||||    | |||    |||| ||  ||  ||     | ||   |  || |    |   || | |  | |  | || |                             
GGAACGAAAGTAAATTTAATTATTACATATTATTCTATGCCTGGAATGACAGGCTATGATCTCCTCAAAAAGATCAAGgtatcttcatttgcctaattattgaatttcaacatcttattattttactccaagttagtcagaacagttcattaaaattaaattttaaataaacatgaatctgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattgtttgatgccagttgatgcatggacacagtatctatctgcatcgctgtcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG