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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag

Basic information

species Glycine max
transcript GLYMA09G04270.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgta---attttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag----------------------
|||||  |||||||||| ||||| ||| | ||||||||  | ||||| |||||||||||||||||||||||||| |||||||   |   | |||| |    | | |  || |    ||     ||| |       ||  |||      | | | ||| || || |                       
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagta-atgtaattttgctactaatatttgagtcat---ttgctt-ccattcacttaatgaaaatattgttgttggaaag------
|||||  | || ||||||||||| ||| | ||||| ||  | |||||||||||||||||||||||||| ||||| || ||||    |||| |   | ||  |||  |  |  | | |   || |   ||||||  | |  | ||     | |  |  ||  |   ||       
GTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTGgtacattgcaaatctgtttagatttcatcttcttctatcgctcctatgttgcttatcgtatagttgcctgataagtaattcctatgaaaatgtag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagt-catttgct--tccattcacttaatgaaaatattgttgttggaaag---
|| ||  |||| ||||||||||| ||| | ||||||||| | |||||||| |||||||||||||||||||||||||||||||       |||    |  | |||    |  | || |||     ||  |  |  | |    | |||   |  ||  | ||  || |   
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttga-gagttcctttttcttgtggtt--tcttggagcatgcttattggtgtacttgtctgatgttgac-ttcctattcaaatgtag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaag-taatgtaattttgctactaatatttga-gtcatttgcttccattcactta-atgaaaatattgttgttggaaag-
|||||| |||| ||||| || || ||| | ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||||||       | | |  |  || |  ||   ||  | || |    |  ||    |||   ||   | |||| ||| | |    |   
GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag-----------------------------------
||||| || ||||| ||||| |||||| | ||||| ||  |||||||||||||||| || ||||| ||||||||||| |||||   |    ||     ||||  || | |||   |   || |||| ||    |    ||     ||||   | | | ||                                      
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgtaaatggttt-tatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctttattaaactctatgcatctacttgtgttggctag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagt-aatgtaattttgctactaatatttgagtcatttgcttccattca-cttaatgaaaatattgttgttggaaag----------------
|||||  | ||||| |||||||||||| | ||||| ||  |||||||||| ||||| |||||||| ||||||||||| |||||   ||   | | |   |   | |||  |||     | |  ||| | |   |||  ||| |      ||||    |  ||                   
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaa--tatttgagtcatttgcttccattcacttaatga-aaatattgttgttggaaag------------------------------------------
|| || |||||||| ||||| |||||| |||||||||||||||||||||||||||| || || || ||||| ||||| ||| |        || |||  |  |   | | |   ||||   | |  | ||| |  |   |   |    | | | ||  | || |                                            
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattc-tactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaag--------taatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag---------------------------------------------------------
|| || || ||||||||||| || ||| |||||||||||||||||||||||||||| || || || ||||| ||||| |||  |    | |            |  |||      |||| ||| || ||||    ||  |||||  || | |   ||||| |  |||  |                                                          
GTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGGgtgggtcatacgaccctgttcctcgggattgaagcgctaacattggattcataacattatattca--tatttattttattgattatgggcaatctcactcgtcccagtttctcacataaaatcgatatgcgttggttttttatgaacag

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag
|| ||||||||||| ||||| || ||| ||||||||||  ||||||||||||| ||||||||||| || || |||||||||||    | ||  |   |  |||  |  | || |    || ||    |  | ||  |                          
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatct-cgagagagacatgttttgtg-tgatgtgaccgtgatcgtgtctcttttgcag------------------------

upper sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag
|| ||||||||||| ||||| || ||| ||||||||||  ||||||||||||| ||||||||||| || || |||||||||||    | ||  |   |  |||  || | || |    || ||    |  | ||  |                          
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatct-cgagagaaacatgttttgta-tgatgtgaccgtgatcgtgtctcttttgcag------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag

- - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA