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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc...

Basic information

species Glycine max
transcript GLYMA12G30520.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc----------------------------------------------------------------------
 |||||||||||||||||||| ||||||||||| ||||| |||||||||||||| || |||||||| || || |||||||| ||| | ||||||||  ||||||||||       ||   | | |  |||| |   ||| |   |||||||||  |  |||  |  | | |  || |       |  |     |  ||||                                                                      
TATGCATCTTGATGCTGAAAAGGAGATGATGTCCCAGTGCGTGGCTCTTCTTGGGAAGTTTATTGCAGTTCGGGAACCAAATATTAGGTATCTTGGTCTGgtaagttgtactttgcaacag-taatactgtttgattctatatatgtttttttggtactttggtaatgtttcgttcacattcctgatagtctataaatgcttcattcgcattaaatccccgtgagtgaaaactttgccataatgtgatggtatttcatctgtcttcacag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtattt--ctcttttcttgtttttttttttttttttttttttctgtttgaagggaggggcaagg-attgcatgc-------------------------
 |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||| || |||||  |||||| |      |||    | |||||| | || ||   |     ||| |  |     | ||  |||    ||   |||       |  |||   ||   ||                           
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaatt------gcatttcttattaatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G700148_T01 (Zea mays), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttttcttgttttttttttttttttttttttt--ctgtttgaagggaggggcaaggattgcatgc----------------------
 |||||||| |||||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||| || ||||||||||| || || ||  |||||| |      |||    | |||||| | || ||      | ||| |     | ||  ||     |     |||   |  | |    | |  ||     |                       
CATGCATCTGGATGCTGAGAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTCGGTCTGgtaatt------gcatttcttattaatatttacttaatgccttttgctggcagtcttgcttccgcatcaagttgtgcaagtgtaaaatctaccatattgagacagtaatcgatccatctttcag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcac-acttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtt-tgaagggaggggcaaggattgcatgc
 ||||||||||||||||| || || |||||||| |||||||| ||||||||||| || |||||| |||||||||| || |||||  ||||||| |||||||| || |   |   || ||||  |  ||||     |  ||    | |||| |    |  ||  |  |||    |  || |      | |||  ||| ||   
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtgagatcttgcataccacttcctgcatctaagcctagctggagtagtttgtgaagtggttggtggtttctcatgatgcattttttgacaaa-attacag--

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaag--ttggggggcacacttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtt-tgaagggaggggcaaggattgcatgc----------
 ||||||||||||||||| || || |||||||| |||||||| ||||||||||| || |||||| |||||||||| || |||||  ||||||| |||||||| ||   | |    | |||||  |  ||||    ||  ||      ||  ||| ||   | |||  |  |   || ||  |         | | |||    |          
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtgagatcttgcatacccacttcctgcatctaagcttagctagaacagtaatttgttaagtatttggtagtgcattatgtggcttctcatgatgcttgttgacaacattgcag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtttgaa--gggaggggcaaggattgcatgc------------------------------------------------------------------
 |||||||| |||||||||||||| ||||||||||| ||||| ||  | ||||| |||||||||||||| || || ||||| || ||||||||||| ||||||||||   ||      | | |  ||||||  |||  || | |  |    | | |    |  ||    |   |  ||  || | |  | | | | | ||                                                                    
CATGCATCTGGATGCTGAAAAAGAAATGATGTCTCAATGTGTTGCCTTGCTTGGGAAATTTATTGCTGTACGAGAGCCAAATATACGATATCTTGGTTTGgtaagttacagga-----tggttctatctgtgcttccgttatgtcttcacctatatccaatgattaaagcatatcaaactggcatgcaccatgttagaatttgaatggattgatgtcattgcttgctgtctaactgcatgatttgacatttagattactctgctgcag

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttt-tcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc
||||||| | || || || ||||| |||||| | || ||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||  |||||   |||     | | ||| |     |    |   ||||  |||||||||   |                                             
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgta---tgg-----atatttg-tggccttacgctatactttaccttgtttttcactgcag-----------------------------------------

upper sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttt-tcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc
||||||| | || || || ||||| |||||| | || ||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||  |||||   |||     | | ||| |    ||    |   ||||  |||||||||   |                                             
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgta---tgg-----atatttg-tggccctacgctatactttaccttgtttttcactgcag-----------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttttcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaggg