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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt...

Basic information

species Glycine max
transcript GLYMA18G02960.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt
 ||||||||||| ||||||||||||||||| |||||||| |||||||| || |||||||| ||  | || || |||||||| || ||||||||| | |||||| ||||   |      |   |  || | |   || |   | ||      | |   || |||  ||||  || | |  ||| |   ||  ||    |   
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacag------gagcaacctgtta--gaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt--
 ||||||||||| ||||||||||||||||| |||||||| |||||||| || |||||||| ||  | || || |||||||| || ||||||||| | |||||| ||||   |      | | |  || | |   || |   | ||      | |   || |||  ||||  || | |  ||| |   ||  ||       |  
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacag------gaccaacctgtta--gaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttgtatag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-----------------atatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttcttt-attcagctgtcatctgatttccagttagaaagtt
 ||||||||||| |||||||||||||| || |||||||| |||||||||||||||||||| ||| | || || |||||||| || ||||||||| ||||||||                 |  || || ||||| |||||||||||  | |  ||  |||    ||   || | ||| | | | |   | |||   | |  |||    ||||      
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgtttta--ttgcaaagtttctatgatatatttctttctgacatacctgctcttt--tttttgtttag------

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 14
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttg-----ttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt--------
 ||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||| ||| | || || || ||||| || |||||||||||||||||| | | || |       |  |   || | |||   ||   | ||   |  |   ||  || | |  || |  ||   | |  ||| || ||   ||    | ||        
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G111355_T02 (Zea mays), 5'ss of exon 5
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttg--ttttttgcctagt--ctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt--------------------------------------------------------------------------
 ||||||||||| |||||||||||| | || |||||||| ||||||||||| |||||||| ||| | || || || ||||| || |||||||||||||||||| | | || |       | | || |   |||   ||   | ||   |  |   ||  || | |  || |  ||   | |  ||| || ||   ||    | ||                                                                          
GGCTAACAGTGCCAAAACATGGAAGAAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataattttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttaggtcgatgatgccttccttacaaagtaaatggtcctctccttgcccccagttatgatctgtttatag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 1
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttgt--tttttgcctagt--ctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcat--ctgatttccagttagaaagtt--------
 ||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||| ||| | || || || ||||| || ||||||||| |||||||| | | || |       | | |  |   |||   ||   | ||   |  |   ||  || | |  || |  ||   | |  |  || || ||   ||    | ||        
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
------------------------------------------------------------------------AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-------------atatg-ttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttcttt-attcagctgtcatctgatttccagttagaaagtt
                                                                         ||||||||||| ||||| |||||||| || |||||||| |||||||||| ||||||||| ||| | || || |||||||| || ||||||||| ||||| ||               ||  ||| ||||| |||| ||||||  | |  ||  |||    ||   || | ||| | | | |   |||||   | |   ||    ||||      
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgtttta--ttgcaaagtttctatgatatatttctttctgacatagctgctcttt---ttttgtttag------

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-atatgttgttttttgcctagtctttgactaaattttgaaatga--actggaatttgtttttctttattca-gctgtcatctgat-ttccagttagaaagtt-
||| ||||||||||| |||||||||||||| |||||||| |||||||| || ||||| || ||  |||| || || ||||| ||||| ||||| || |||||  |||  |      |  ||||||    ||  || ||||  | | |  | |||  ||   |||   || |  | ||  |  | | || ||   ||     | |  
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCTGAGGAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAGgtggataaataacagat--cctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgttttt-----ctttat---tcagc---tgtcatctgatttccagttagaaagtt------------
||| ||||||||||| |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || |||||||| ||||| ||||| |||||||| | ||      | || |  ||      | |      | | | |   | || ||   || |     ||||||    ||     | |||| |  || |  ||||     ||            
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGCGTTGATGCTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtga-atacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgtttttt--gcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt------------------------------------------------------
 ||||||||  |||| ||||||||||| ||||||||||| |||||||| || || ||||| || || || ||||||||||| || || |||||||| |||||||| | |||||||||  |  |||  |  ||  | |   | | |  ||  |    ||||||     | | |  |||| ||  | || | ||    |   ||                                                      
GGCTAACAGCTCAAAGACATGGAAGGAGGTTTGCTTTGCTTGTGTTGATGCAGAAGAGTTCCGCTTAGCTCAGATATGTGGTCTCAACATTATTATACAGgtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgt-atgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 5'ss of exon 25
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttg-aaatgaactggaatttgttt--------ttctttattcagctgtcatctgatttccagttagaaagtt------------------
||| || ||  | |||||||||| ||||||||| ||||| || || ||  | ||||| ||||| ||||| || || ||||| ||||| || |||||||||||| |   ||  |         || |   ||  |||||     |||||     || | ||           |  |    || |    | ||| ||  | | | |  |                    
AGCAAATAGCTCTAAAACATGGAGGGAAGTTTGTTTTGCTTGCGTGGATACCGAGGAATTTCGGTTGGCTCAAATTTGTGGCCTTAAGATCATTATTCAGgtattggcttagtcaacataatgtatcatacagaatttaatggatgaaacctgatatcttcaggatcaacaccatgcctagttcatttttgaatttgaatgaaatgggctttttgtggctgtggaag

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt
 || |||||||| || || ||||| ||||||||||| || |||||||||||||| |||||  |  | || || |||||||| || ||  | ||| | |||||||     |  ||| ||  ||  || |      || ||    ||  ||  ||| |||| ||    || |||                            
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAGgtaaggctatagtttctggttatactct------atctttggttggtct--aatctgttattaa--atccag----------------------------

upper sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
lower sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt
 || |||||||| || || ||||| ||||||||||| || |||||||||||||| |||||  |  | || || |||||||| || || || ||| | |||||||     |  ||| ||  ||  || |      || ||    ||  ||  ||| |||| ||    || |||                            
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactct------atctttggttggtct--aatctgttattaa--atccag----------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG