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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG

Basic information

species Glycine max
transcript GLYMA12G29800.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 9
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttac-ctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
                ||        |||   | |  ||  ||     |    |        |||| || | || ||  |  |  ||     ||| |   | | |||      |  |||||||| |||||||||||| |||| || ||| | || || ||||| ||||| ||||| |||||||||
----------------acatgaaggaaaaacagcaacggcataacaaaacggaaggaggatcagatgttttctttttcttaaaactatccgtcttcacattctgtttcaca--tgcagATTTGTTGAAATTATGGCAACTGTGTTCTCTAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
    |  |     |  || ||  |||    |   |||  | | |   |   | |  |||  |    | ||| | |   | | |      |  | | || |  |  |||       || ||||| || |||||||||||||| |||||| | ||||| ||||| ||||| ||||| |||||||||
----gtacggctctgtactctctttc----tctcattc-tctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgc------agGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtc--tacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
                      ||      |||||  | | | ||  || | ||  |  | ||| | | |  || |||||  |||| ||||  ||  |  | ||    | | |    || ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||| |||||||||
------------------gtaagtctctctttgaaacgttctctt--tagagcaact--caagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcac---agGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------gtatgctctctcttccaccctgg---ttcaaag--ttgaattggtgtattgctatatcattt----acctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
                                                                          | ||   | |  |   |   |     ||||||   ||| |     |  |   ||| |  | |    || |  |||||||   || |  |  |||||      |||   | |  |   ||| || |||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| |||||||||
gtatgctttctctctgttctccctctcttgcatatctggtgtgcgtgaatttgtctttatgagtgttaaaacatgcataaacacaatgtaaaaataaatattcaaatatttgtaacatagggtaaatatgttgtcttgggacttgcattttctcccctctcccctcttagg----cttacagttttctacattaattcagATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAG

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|51343480|gb|CO984213.1|CO984213
EST:     GAAGAGAAACCAGGCTGGTGTAGTGATCCACATTTGCCTCCTTGTGCTGC                         ATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGT
genomic: GAAGAGAAACCAGGCTGGTGTAGTGATCCACATTTGCCTCCTTGTGCTGCgtatgctctc ... gttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGT
EST: gi|51338123|gb|CO981989.1|CO981989
EST:     GAAGAGAAACCAGGCTGGTGTAGTGATCCACATTTGCCTCCTTGTGCTGC                         ATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGT
genomic: GAAGAGAAACCAGGCTGGTGTAGTGATCCACATTTGCCTCCTTGTGCTGCgtatgctctc ... gttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG
                       agttaac  putative branch site (score: 3)
                                       tcttttgttatttt  putative PPT
                  tacttagttaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC