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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatgtaatgtctaaagcaaattgatttgaacgattgtttaaaagctagagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT

Basic information

species Glycine max
transcript GLYMA02G08180.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G24170.3 (Arabidopsis thaliana), 3'ss of exon 11
------------------gaatgtaatgtctaaagcaaat--tgatttgaacgattgtttaaaagctagagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT
                     || |    |||||    ||  ||| |  |    |   | |    || | |||  ||| |  | | |    |||    ||| ||    | || |  | |||| || ||||||||  | || |  |||||||||||||||||||| || |||| |||||||||||| || ||||| || || || || ||||| ||  | |
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctc-ctcttgcagctactaattcagta---cattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT

upper sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 12
gaatgtaatgtc-taaagcaaattgatttgaacgattgtttaaaagct---agagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT
     |  | || | || || | |  |||      || ||||     |   ||   |  |   | |     ||    || |  ||  || |  |||   |  |||| |||||||| ||| | || | ||||||||||||||||||  | |||||||| ||||| |||||||||||||| || |||||||| ||||| | | | |
tcccctgttctcatgaaacagaattttttatttatttatttatttttttccagcataaaaagttaataaccagactgaagttctcc-tgttgtttt---tccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT
















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|37996094|gb|CF807683.1|CF807683
EST:     TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAG                         GTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
genomic: TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAGgttcacatct ... ttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
EST: gi|192306241|gb|FG995063.1|FG995063
EST:     TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAG                         GTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
genomic: TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAGgttcacatct ... ttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
EST: gi|23052788|gb|BU577279.1|BU577279
EST:     TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAG                         GTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
genomic: TGAATTTAGAAGCTGTTGGTGTTGAGCTTGACAACACTGGAGCAATAAAGgttcacatct ... ttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
EST: gi|192328962|gb|FK019689.1|FK019689
EST:     GGAGCAATAAAG                         GTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT
genomic: GGAGCAATAAAGgttcacatct ... ttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT
                        ttctaaa  putative branch site (score: 2)
                                         tcctttgt  putative PPT
      aatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatgtaatgtctaaagcaaattgatttgaacgattgtttaaaagctagagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
gaatgta
- - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtg