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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttattattgttacaacttcgaa...

Basic information

species Glycine max
transcript GLYMA02G42560.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 23
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctc-taaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttatt---attg-ttacaacttcgaa
| ||||| ||| | || ||||| |||||  | || ||||| ||||| ||||||||||| ||||||||||| ||||| ||  ||||||| |||||||| |||| ||     | | ||   || || ||   |   | | || ||     ||  |  | ||  | || | |||||||  |   ||    || | ||  || | | | 
GGGATCCTACCCTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaattgtttttattcttcataccttttaattttatttcttctga--atctttaaatccatctattgattgcttacatagaaatcgatttgaattgccag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 23
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgatt-attgttattattgttacaacttcgaa-------
| ||||| ||| | || ||||| |||||  | || ||||| ||||| ||||||||||| ||||||||||| ||||| ||  ||||||| |||||||| |||| ||     | | ||   || ||  |  |   | | || ||     ||       |  ||| | |||| |||| |||| |   || |  |    || |||       
GGGATCCTACCCTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaattgtttttattcttcatacttttaattttatttcttctga------atctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 12
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgaga-gtatactttgcaggataaagtgtagttacaaccattgattat-tgttattattgttacaacttcgaa------
  ||||| ||  | || ||||| |||||| | || || || ||||||||||||||||| || ||||| ||||| ||||| || ||||| |||||||| |||| |||  |  || ||   |  | | |  || ||    |  ||       |  |    | ||      |    |||  ||||  |||||     | ||  ||      
--GATCCTACACTTGCTGTTGTTGCTTATAGACGTGGGCAGTGTGACGATGAACTTATTAACGTCACTAACAAGAATTCGTTATTCAAGCTGCAAGCTAGgtatgtaata-atttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtc-tgacgacttacatgttcatattgcatttatttaaaatgacag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 9
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgaga-gtatactttgcaggataaagtgtagttacaaccattgattat-tgttattattgttacaacttcgaa------
                                || || || ||||||||||||||||| || ||||| ||||| ||||| || ||||| |||||||| |||| |||  |  || ||   |  | | |  || ||    |  ||       |  |    | ||      |    |||  ||||  |||||     | ||  ||      
-------------------------------ACGTGGGCAGTGTGACGATGAACTTATTAACGTCACTAACAAGAATTCGTTATTCAAGCTGCAAGCTAGgtatgtaata-atttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtc-tgacgacttacatgttcatattgcatttatttaaaatgacag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 21
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcagga-taaagtgtagttacaaccattgatta-ttgttattattgttacaacttcgaa------
| ||||| ||  | || ||||| |||||| | || || ||||||||||| || ||||| |||||||| |||||||| || |||||||| || ||||| |||| | |  | ||| || | |||| | |     |  | |  ||||    | |    | ||  |  | | || | |   ||| |  | |      || ||  ||      
GAGATCCTACACTTGCTGTTGTTGCTTATAGACGTGGGCAATGTGACGACGAGCTTATTAATGTCACTAACAAAAACTCATTGTTCAAGCTACAAGCTAGgtatataat-tatttttgttcctgttactgatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtcatgtcacataaatttaaaatttcag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 23
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttat-tattgttacaacttcgaa
||||||||||  | || ||||| || ||  |  |||||||||||||||| ||||| ||||||||||||||||| || |||||||||||  | ||||| |||| | || |   |||||  | ||  |         |||| |   ||          |||||||     | || || |   |     | || ||||| |   
GTGATCCCACTCTGGCTGTTGTGGCATACAGAAGAGGACAATGTGACGAGGAACTCATCAATGTCACCAACAAGAACTCTTTGTTCAAGTTACAAGCCAGgtatttgat---tattgcttactagacttcttacttatattccacac---------tagttact-ttgtagactacttacacacgattttccaactgcag-

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 23
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagt-gtagttacaaccattgattattgttattattgttacaacttcgaa
||||||| ||| |||||||||| || ||  |  |||||||||||||||| ||||| ||||||||||| |||||||| |||||||| ||  | ||||| |||| | |    |||  |  ||     ||| |     ||  ||    | | | |  | ||||||      | |    |   ||   |||||            
GTGATCCTACCCTAGCAGTTGTGGCATACAGAAGAGGACAATGTGACGAGGAACTCATCAATGTCACTAACAAAAACTCTTTGTTTAAGTTACAAGCCAGgtattt----tatcattacttacgaaaattcttgttactctcacaatggtgactttgtagttt--gttaatacacaagttttcaattgtag----------

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 23
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttattattgttacaacttcgaa
||||||||||| | |||||||| ||||| ||| |||||||||||||||| |||||||| |||||||| || || || |||||||||||||||||||| |||||||||   | | ||   |||    |  | |   ||| | |    ||||  | |      |    |  |  |||    || |    || ||        
GTGATCCCACCCTCGCAGTTGTTGCTTACCGGAGAGGACAATGTGACGAAGAACTTATAAATGTCACAAATAAGAACTCTTTGTTCAAACTGCAAGCCAGgtttgtgacttgt-ttacttcccgatatattatcatatgcat----ggattcatttggtacatggacgctacttacacatacttccatttcag-------

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 11
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataa--agtgtagtta--caaccattgattattgttattattgttacaacttcgaa
| ||||| ||  | || || || || ||    || || |  ||||||||||||||| |||||||||||||||| |||||| | || || || || || ||||        |    | | |  |||   | |     |    |  || | |||  |   || |    ||||   | |      | | |  |||| |  |||    
GCGATCCAACGCTTGCTGTGGTTGCATACAAACGTGGCCTGTGTGACGATGAACTTGTCAATGTCACCAACAAGAATTCTCTCTTTAAGCTTCAGGCCAGgtaaacaagatcggattgtttatctgttg-gttttgacgagtcacatgttaatcatcttaatcgttcaactcgttacctgaataacttgtgtttctgctta---

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 23
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 11
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgt--------ttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttattattgttacaacttcgaa
| || || ||  | || || ||||| ||    || ||  | ||||| ||||| ||| |||||||||||||||| |||||| | |||||||| || || ||||        || |  || ||| ||  | ||||    | ||  |  || ||||| | |  |      |||      |  | ||||  ||||||| |   |   ||   
GCGACCCAACTCTTGCTGTGGTAGCATACAAACGTGGCAATTGTGATGATGAGCTTGTCAATGTCACCAACAAGAATTCTCTCTTCAAACTCCAGGCCAGgtgaaaatgattctactg-ataatgtgtgctctttgataagt-tccacgttgcaaggttgaaacacattatg----tgaagtatttgtattattatcttattgtca--

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATCCCACCTTAGCAGTTGTAGCTTATCGGCGAGGACAATGTGACGATGAACTTATCAATGTCACCAACAAAAATTCTTTGTTCAAACTGCAAGCAAGgtttgtggtgtatattggctcctctaaagtgagagtatactttgcaggataaagtgtagttacaaccattgattattgttattattgttacaacttcgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG