Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtctctttgttcttgtaaactcatcatattatcgctgacatgtttgcagctccttcacttcacacatatttttaacttgcctccactttgatctttag

Basic information

species Glycine max
transcript GLYMA08G20020.1
intron # 36
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 36
lower sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 9
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtctctttgttcttgtaaactcatcatat-tatcg--ctgacatgtttgcagctccttcacttcacacatatttttaacttgcctccactttgatctttag
|||||| |||||||| || |||||||| ||||| |||||| |||  || || || |||||||| ||||||||||| |||||||| || || || |||||||| |||      | ||| |  ||  | |  |  | | | | |  |||  |   ||| | || | ||  | ||                                    
ATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAGCAAAGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaa-----ttatgtaccagtggattttttttttgtcttgatctgctaaacttgta-ctgcctctttccag-----------------------------------

upper sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 36
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaag-----tctctttgttcttgtaa-actcatcatattatcgctgacatgtttgcagctccttcacttcacacatatttttaacttgcctccactttgatctttag
 ||| | |||||||| || |||||||| || || |||||| | ||||| | |||||| ||||| ||||| |||||||||||||| ||||| || |||||||| ||| |     | || |  |   |  || ||||| || |   | | |        ||| | |  |   || ||                                    
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactca-caaagcgttgtttgttataatgcgg-tgttcttctgcag-----------------------------------

upper sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 36
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 5'ss of exon 37
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtctctttgttcttgtaaactcatcatattatcgctgacatgtttgcagct-ccttcacttcacacatatttttaacttgcctccactttgatctttag----
 ||| | |||||||| |||||||| || |||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| |||||||| |||||||| || | ||   |  ||    | | ||   |    |     | || |     |  |   | |||||||   |   ||       ||  | | |||||   ||       
GTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGGCAAAAACCATTGATCTTTGCAACAATCCCATGACAAAGGAACCCAAGCTTCAGgtaaacattcatatccttgagcttatcttccctctcttcaaataactttaccaccaccgtcatcacttctttccctttccatttctgtttgctctttgtcattctcccag

upper sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 36
lower sequence: PP1S25_65V6.1 (Physcomitrella patens), 5'ss of exon 18
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtctctttgtt-cttgtaaactcatcatattatcgctgacatgtt-tgcagctccttcacttcacacatatt--tttaactt---gcctccactttgatctttag---
||||||||||||||||||||||||||| || || || || ||  |||| || || || ||| |||| |||||||||||||| || || || || ||  | || |    |   ||  ||  |||| | | | ||    | || ||  ||| |    |  || || || ||   |  | ||  | || | |     | ||||  || | | |     
ATGGCTTTGGTGTGAGTCATGGTGTGGGAACGCAACCAAGTCTCAGGCTAAGACTATCGATTTGTGTAACAATCCCATGACGAAGGAGCCTAAGCTAGAAgtaagtcatgatttaattatttgttaccacttctctctctctctctcatttcgcccgacttctacagttataatttcttactgtagcctttgatccccacgctgttttctcacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15204868|gb|BI427636.1|BI427636
EST:     AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAG                         GGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
genomic: AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtc ... tgatctttagGGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
EST: gi|112361150|gb|EE400121.1|EE400121
EST:     AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAG                         GGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
genomic: AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtc ... tgatctttagGGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
EST: gi|22523540|gb|BU082360.1|BU082360
EST:     AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAG                         GGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAG
genomic: AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtc ... tgatctttagGGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAG
EST: gi|20812577|gb|BQ297055.1|BQ297055
EST:     AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAG                         GGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
genomic: AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtc ... tgatctttagGGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
EST: gi|12690009|gb|BG156345.1|BG156345
EST:     AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAG                         GGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT
genomic: AAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtc ... tgatctttagGGTGCAAGACGAATAGTATCAGAGTGGCCAGACCTTGATTTGGAGGCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaagtctctttgttcttgtaaactcatcatattatcgctgacatgtttgcagctccttcacttcacacatatttttaacttgcctccactttgatctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC