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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttttctttgtattttttattcatgctggttcgtaattattgtgatattctttaagtgtttctgagatcatcatccattaaaagcatgattgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGGAAGAAGCTCTTGCAAAAGAAG

Basic information

species Glycine max
transcript GLYMA16G27210.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G24170.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttttctttgtattttttatt-catgctggttcgtaattattgtga--tattctttaagtgtttctgagatcatcatccattaaaagcatgattg-tgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGGAAGAAGCTCTTGCAAAAGAAG
|||  |   || |  |||    |  |||    |    ||||  ||| |  |       || ||| | |||     |   |  ||    |  | | || || |||||||| |  ||||||||||||||  | | ||||||||| |||||||  ||||||||||| ||||||||||||
gttcctaaattattgtttaggctatatgtctatgaacaattcatgtcaactgagagagaattgtgtttgatgatgtatactgtt----gtttaactgctggcagGATGCTAAAAATTATGGGTGGGAAATAAATGAGAAAGTCGACTTCACATGGAAGAAGCTTTTGCAAAAGAAG

upper sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 5
gttttttctttgtattttttattcatgctggttcgtaattattgtgatattcttta----agtgtttctgagatcatcatccattaaaagcatgattgtg--acagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGGAAGAAGCTCTTGCAAAAGAAG
    ||||  || |||||| || ||   | ||  |  ||  |   ||| ||| ||     |  |||||||| || |||    |   || | |||  |||     ||||||||| ||||||||||||||| |||| ||| ||||| ||||| || ||||| || || || || ||||||
----tttccatgcatttttcatgcaa--tagtatgatatattcaagattttccttgtcataaggtttctgacattatctgatacgtaatgtatgtatgttttgtagGATGCCAAGAATTATGGGTGGGAATTGAATGACAAAGTGGACTTTAACTGGAAAAAACTTTTACATAAGAAG
















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|298193865|gb|HO040513.1|HO040513
EST:     GGAGCATCTTTTGGAGGTGATCTTGAG                         GATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG
genomic: GGAGCATCTTTTGGAGGTGATCTTGAGgtaaggattt ... attgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG
EST: gi|27424557|gb|CA936077.1|CA936077
EST:     TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG                         GATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG
genomic: TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAGgtaaggattt ... attgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG
EST: gi|193346232|gb|FK309724.1|FK309724
EST:     TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG                         GATGCCAGGAATTATGGGTGGGAGTTGA
genomic: TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAGgtaaggattt ... attgtgacagGATGCCAGGAATTATGGGTGGGAGTTGA
EST: gi|151394106|gb|EV263977.1|EV263977
EST:     TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG                         GATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG
genomic: TTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAGgtaaggattt ... attgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattctttaagtgtttctgagatcatcatccattaaaagcatgattgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGGAAGAAGCTCTTGCAAAAGAAG
                                 attaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttctttgtattttttattcatgctggttcgtaattattgtgatattctttaagtgtttctgagatcatcatccattaaaagcatgattgtgacagGATGCCAGGAATTATGGGTGGGAGTTGAGTGAGAAAGTTGACTTCAATTGGAAGAAGCTCTTGCAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcca