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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA

Basic information

species Glycine max
transcript GLYMA10G21350.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G047310_T02 (Zea mays), 3'ss of exon 4
atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA
              |   | |||  ||   |     ||  | |   | |||  | ||       | |  ||  |||   ||  |||| || || | | ||||||| ||||| ||||||||||| || || ||||||||||||||    ||||| || |||||| | || || |||||| |||||||  | || || ||||
------------gtacacacttgtgaa---cttaaattccgtgttattatatgtact-------agtcttagccttccttgtgactgtttgtattgc-agGATGAAGCTGGGACTGCAGCCATCAAGACAGTTGAACTTGATGCCATCCTTGGGGGTCGTGCAATTCAACATAGGGAACTCCAAGGTTACGAATCTGACA

upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA
        || || | ||  ||||  | |  ||    ||  | | |  | | |||  | | ||  || |    ||   |||  | ||||   | ||| ||||||| |||||||| |||||  | || || |||||||||||||| ||||||||||| || || || ||  |  | ||||| ||||| ||||| || ||||
--------gtatttattt--ttgggcatgatagcatatattacgttctaaatttgaatcgtcattatta----ctaatctgcgattgat---aattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA

upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 3
--------atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA
        | ||   | ||||   |||||  ||||   ||   ||    |     | |   |||||     ||||   ||  |         ||| | ||| |  ||||||||  ||||||| ||||| || ||||||||||| |||||| ||| |||||||||||||||||| || ||||| ||| | |||||  | ||||| ||||
gtattactacttccttttgtt--cttattcagaaattacacttgtagtaaaataacgtttatgctt----gaaattgcaactt---------ctggtctta-tcatagGATGAATCTGGAACAGCAGCTATAAAAACTGTTGAGCTTGATACTGTTCTTGGAGGGCGTGCAGTACAACACAGAGAACTTCAAGGCTACGAGTCTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA
                                     cactgat  putative branch site (score: 3)
                                           ttttacttct  CT-rich tract
           tttgacaaaataataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG