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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatgttaatttctccgcctattctttcttctttttttccatcattacgcttgctggtttacag

Basic information

species Selaginella moellendorffii
transcript EFJ30909
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatg-------ttaatttctccgcctattctttcttctttttttccatcattacgcttgct-----ggtttacag------------------------
| ||| || ||| | || || ||||| ||| | || |||||||| ||||| |||||||||||| |||| || ||| | || ||||||||||| || ||||||||        | ||||  |  |   |  ||||  |   | || || |  ||    |||||     || || |||                        
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg

upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 9
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtat-gttaatttctccgcctattctttcttctttttttccatcattacgcttgctggtttacag------------------------------------
|  || || ||| | || || ||||| ||  ||||||||||||| ||||| |||||||||||| ||||||| ||| | || || || ||||| ||||||||||| | |  ||      |||||  |   |     | ||   | |||  || |  |  |  | |                                     
AGCACATTTCATCGTTTTGACAAATTCAATCTAAAATACAATCCATGTGGCCAAAGTAGGCTCAGAGAAATTTTCCTCAAACAAGATAATCTTATTCAAGgtattggttgttataagtcctatattccttaaaagtcttttttgattgggcctttta-tgcaaattcctttatttattgtatattatcatgctcattgttc

upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA01G29470.1 (Glycine max), 5'ss of exon 10
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgta-tgttaatttctccgccta----ttctttcttctttttttccatcattacgcttgc--tggtttacag-----------------------------
| |||||| ||| | || ||||| || ||  | |||||||||||||| || |||||||||||| | || |||||  | |||||||| ||||| ||||||||||   ||  ||| |  |  ||    | || ||  || | || |  | || |   |     ||| | | |                              
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGCGGTCAAAGTAGGCTCAGGGAGATATTTCTTAAGCAGGATAATCTCATTCAAGgtaacatttttttttgggtataacagtcctatcacctgtgttactttaatcaaattcaaagtggctgaaatatcccatggttttgtgcagtatttttact

upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 9
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgta-tgttaattt--------ctccgcctattctttcttctttttttccatcattacgcttgctggtttacag---------------------------
| |||||| ||| | || ||||| || ||  | ||||||||||||||||| |||||||||||  | || |||||  |||||||||| ||||| || |||||||   ||  |||        | | | |   ||   | | | |||     | || |   |    ||   | |                            
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGTGGTCAAAGTAGGCTGAGGGAGATATTTCTGAAGCAGGATAATCTCATACAAGgtaacatttttttgggtataacactgtcctatcacacctgtgtttacttgtaatcaaattcaaaggggcagaaatatcctatggttttgtgcagctttct

upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 9
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatgttaatttctccgcctattctttcttctttttttcc------atcattacgcttgctggtttacag------------------------------
|  || || ||| | || ||||| || ||  | || |||||||| || || |||||||||||| | ||||| ||| | |||||||| ||||| || |||||||||      |       | ||  ||    |    ||        |    ||  |   |   |||  |                               
AGCACATTTCATCGTTTTGATAAGTTCAATCTCAAGTACAATCCCTGCGGTCAAAGTAGGCTCAGGGAAATTTTCCTTAAGCAGGATAATCTTATCCAAGgtatggcgtgcttgttatatgtttattaggttaagcttgaggaaaaagtgctaaacagacccttttgaacaagtttttttcaatttccaaatacttcatt

upper sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 5'ss of exon 9
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatgttaatttctccgcctattctttcttctttttttccatcattacgcttgc--tggtttacag-----------------------------------
||||| || ||  ||||||| || || ||||| || || ||||||||||| || ||||||||  | ||||||||| | |||||||||||||  || |||||||      | | || |   | || |     ||  |||  |||   | ||||||  || | |  |                                    
AATACATTTCACCGATTCGACAAGTTCAACTTGAAGTATAATCCTTGTGGCCAGAGTAGGCTAAGGGAAATATTCCTAAAGCAGGACAATCACATCCAAGgta-acgcgtctttcagggaagtcctcagaattagtttgaatctacatgcttgcgatgatgtgaaatcactcacaattattcgaatgatgttcacttttgc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatgttaatttctccgcctattctttcttctttttttccatcattacgcttgctggtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC