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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttccttttggcttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ37510
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcat--tttccttttggcttgcag-------------------------------------------
||||||| ||||| || || |||||||| || ||| | | |||||| |||||||||||||| |||||||| |||||| |  | || ||||| ||||||||||    | | ||    |||| | |    | |  | | |||  |||  ||||  |     |                                           
GGATGGGATTCATTCAATCCAATCACTCTGTTATCATGTACAACAACACCATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgta---acttttgaactggtgctggctctgtaaatcccatgttttatttttcaccaattgatgctataggatgctaagatctgttaaggtatataaagcctat

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttgga--gctcattttccttttggcttgcag-----------------------------------------------
| ||||| ||||| ||||| || ||||| || ||| | | |||||| ||||||||||| |||||||||||||||||  | || |||||||| || || ||||  || |   ||||||  ||      ||||  |  | |   | ||   || || ||                                                  
GTATGGGGTTCATTCAGTCCAACCACTCTGTGATCATGTACAACAACACCATGATCAGTTTCAACATGCTCGAGGCTGCACGTATCAATGGTGTGAAGAGgtccggctctctcttttttttttacatatttttactgttatatctcagcttagcctgagcttgttttatccatatcaattcatttgttacaactaatggtcctacag

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G138907_T01 (Zea mays), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcat-tttccttttggcttgcag-----------------------------------------
||||||| ||||||||||| || ||||| |||||| | | |||||| |||||||||||||| |||||||| |||||  |  |||| || || ||||| ||||          ||   |||  |     ||||    ||||   | | |||  | ||  |                                         
GGATGGGGTTCATCCAGTCCAACCACTCCGTCATCATGTACAACAACACCATGATCAGCTTTAACATGCTTGAGGCTGCTAGAATTAACGGCGTCAAGAGgtaatttccagcctcaaggtagctgctctttgtttatcatgcgtgcatttaccctggtgagctagtttcatatatattgcctccagtgctaaatctgttc

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttccttttggcttgcag-----------------------------------------------------------------------------------------
| ||||| ||||||||||| |||||||| || ||| | | |||||| ||||||||||| || |||||||| |||||  | || |||||||| || || |||| |  || |   | |           |||   |  |||||||| || ||||| |                                                                                            
GCATGGGGTTCATCCAGTCAAATCACTCTGTGATCATGTACAACAACACCATGATCAGTTTTAACATGCTGGAGGCTGCACGTATCAATGGTGTGAAGAGgtatatatacaaatat-----------attgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcag

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttccttt-tggcttgcag---------------------------------------------------
||||||||||||||||||| || |||||||||||  | | |||||| |||||||| |||||||||||| | |||||  || | |||||||| || || ||||    |||| | ||       |  |  ||   |  ||| ||||  ||      |  ||                                                   
GGATGGGTTTCATCCAGTCCAACCACTCGGTCATTATGTACAACAACACCATGATTAGCTTCAACATGATTGAGGCTGCCAGGATCAATGGTGTTAAGAGgtc---attcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttag

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA19G43400.1 (Glycine max), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttcc-ttttggcttgcag----------------------------------------------------
|||||||||| |||||||| || ||||| |||||  | | |||||| |||||||| |||||||||||| | |||||  || | |||||||| || || ||||    |||| | ||       |  |  ||   |  ||| ||||  ||      |  ||                                                    
GGATGGGTTTTATCCAGTCCAACCACTCAGTCATTATGTACAACAACACCATGATTAGCTTCAACATGATTGAGGCTGCCAGGATCAATGGTGTTAAGAGgtc---attcattttaaacaaacatgtgttattatgtcactttcaattgcataatatagtctttatgtcgctgtcatagtgatccttgttttttggtttattttttttaag

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA19G43410.1 (Glycine max), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttcc-ttttggcttgcag-----------------------------------------------------
|||||||||| |||||||| || ||||| |||||  | | |||||| |||||||| |||||||||||| | |||||  || | |||||||| || || ||||    |||| | ||       |  |  ||   |  ||| ||||  ||      |  ||                                                     
GGATGGGTTTTATCCAGTCCAACCACTCAGTCATTATGTACAACAACACCATGATTAGCTTCAACATGATTGAGGCTGCCAGGATCAATGGTGTTAAGAGgtc---attcattttgaacaaacatgtgttattatgtcactttcaattgcataatatagtctttatgtcgctgacatagtgatccttgttttttggtttatttttttttaag

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 5'ss of exon 2
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattctt-------cttttggttccgagaatttggagctcattttccttttggcttgcag------------------------------------
| ||||| ||||| ||||| |||||||| || ||| | |  ||||| || ||||| |||||||||||||| ||||| ||  |||||||||| || || |||| ||  | |||       ||  |  ||   ||  ||   || || ||| |   |||  |||                                       
GTATGGGCTTCATTCAGTCCAATCACTCTGTTATCATGTATAACAACACAATGATTAGCTTCAACATGCTTGAGGCTTCAAGAATCAATGGGGTTAAGAGgtttgtctccttggattcactacttatttttagctttatcagttc-tttccaagttgatttgagaattatctactatttgaaaccaaagaatacttttttg

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S171_56V6.2 (Physcomitrella patens), 5'ss of exon 1
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttt-tggttccgagaatttggagctcattttc----cttttggcttgcag-------------------------------------
| ||||| ||||||||||| |||||| | |||||  | | |||||||||||||||||||||||||||||| || ||||| || |||||||| |||   |||||     || ||| |    |||| |   |        ||||| |    ||||   |||||                                       
GCATGGGCTTCATCCAGTCCAATCACGCTGTCATTATGTACAACAATACCATGATCAGCTTCAACATGCTTGAAGCCTCACGCATCAATGGTGTCTCTAGgtgcatgctcctctctgcccttccaattttaccttagccatttccagctctttattcttgctttcgaaggtctctgcttatgtgcaatctctgtttctct

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S98_250V6.1 (Physcomitrella patens), 5'ss of exon 1
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGG--------AGTCAAAAGgtgtggattcttcttttgg--ttccgagaatttggagctc---attttccttttggcttgcag-----------------------------
| ||||||||||| ||||| || ||| | || ||| | | |||||| |||||||||||||| ||||||||||||||| | || ||||||||         ||    |    | |   |||||||| |  |  |      | | |||||   || ||| ||| |      |                              
GCATGGGTTTCATTCAGTCCAACCACGCCGTGATCATGTACAACAACACCATGATCAGCTTTAACATGCTCGAGGCCGCGCGCATCAATGGCGTCTCTCGgttggcaacccttgccccttctttttgcctctctccctctcgcagctctggatcttcttttcgaaaaaaaaacacacagttaacaatgaatgtttctttg

upper sequence: EFJ37510 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S237_14V6.1 (Physcomitrella patens), 5'ss of exon 1
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttcc--gagaatttggagctc-attttccttttggct-tgcag--------------------------------------
| ||||| ||||||||||| || ||| | |||||  | | |||||| ||||||||||| |||||||||||||| ||| | || ||||| || || |   |||| |   |||     || || |      |||   || || ||||||  || | || |||                                        
GTATGGGCTTCATCCAGTCTAACCACGCCGTCATTATGTACAACAACACCATGATCAGTTTCAACATGCTCGAAGCCGCTCGCATCAACGGTGTTACCCGgtgcgcgctctcgcagtgctttctttgccattaccagttcgattttcacttcgtctctgccattagtgggaattttgtttcttttattcctaattgcgtt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGGTTTCATCCAGTCGAATCACTCGGTCATCCTTTTCAACAATACCATGATCAGCTTCAACATGCTCGAGGCCTCCCGAATCAATGGAGTCAAAAGgtgtggattcttcttttggttccgagaatttggagctcattttccttttggcttgcag

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