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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaaatcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC

Basic information

species Glycine max
transcript GLYMA01G38580.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaaatcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC
        |||   | |||   ||| || ||    ||  ||  ||     || ||  | | |  || ||   | ||  || | | ||  || |  |   ||||    |||| | ||  |||| ||||| || || |||||  | ||||| ||||| ||  | |||||||||||||||||||||||||| || ||| | || || || |||||||||||||
--------gttcagaaggtagttgtgtgtttc---gactctgttaattcgtgcgt-cgttcctcataataggttga--gtatgagaatggttaatt---cttt---tttcttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC

upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaa-atcattcttggaaagt-tttaaaactgtg--acctaaactttgaa----cttctggcttt------tagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC
|||   ||  | | |||  || |  ||  || | |  |  || |  || |||    || ||||  ||  |  ||| |  |  |  |   |||    |  | |||  || |    ||| || ||||      ||||| ||||| ||||| ||||||||||| || |||||  |  ||||||||||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtacaattactgtaaggagttat--ttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC

upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 21
gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaaatcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC
                                                || || |     ||||  ||||  | |     | || ||  ||         |||||| ||      || |||||||||||| |||||| | ||| || || || ||  | |||||||||||||| ||||| ||||||||||||  ||| || || || ||||| ||  | |
-----------------------------------------------gtacggat-----tcaatgcatttgttg----ctctataatcgt---------tttgaaatt------ttcagGTCAATCCTGCAAACGCACATCTGGTCGTGGGCCAACTTTTAGATGATGAATGTCCTGAGGATTTTATTAAAAATCTCATCCTCTCTGTTCGATCGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC
                           acctaaa  putative branch site (score: 3)
                                         cttct  putative PPT
          aaagttttaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaaatcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA