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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgaaaatttgtgttattcgtgctttacacccaataggtaataacattaggaggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG

Basic information

species Glycine max
transcript GLYMA10G00550.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
-----------------------------------------gtaaaatgaaaatttgtgttattcgtgctttacacccaataggtaataacattagg--aggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG
                                         ||    |||  |||     | ||| || | |     || | |  ||||   |   |   |||||   || ||      || |  |  || | || |    ||||||||||| ||  | |  || |||||||| ||||| ||||| || ||||||||||||||||||||||  ||||   | || |||||  || |
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgtttt----cagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG

upper sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
----gtaaaatgaaaatttgt--gttattcgtgc-tttacacccaata--ggtaataaca-ttaggaggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG
    | ||  |  | |  | |   | | |      |||  | ||  |   ||||   | | ||   |  |   | | |||  |||| ||    || | | ||     ||||||||||||||| ||||| ||| |||||||||||||||| ||||| || ||||||||||| |||||||| ||||| ||||   | ||| ||||
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttacc--gcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG

upper sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 15
gtaaaatgaaaatttgtgttattcg--tgctttacacccaataggt-aataacattaggaggattacctgtctcacttctacaagactata---tcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG
|||||| | || |   ||||   |   | |  |    |||||   | |||   ||  | | | |||  |||  ||||| |     | ||||   |   ||||| ||||||||||| ||| | |  |||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| |||||| | ||
gtaaaaggcaattggttgttgagcaattacagttgttccaattaatgaatcttatctgaaaggtta--tgttccacttatcacgtaatataaatttccgtttgacagATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG

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|6747416|gb|AW317872.1|AW317872
EST:     GATGGGATGAAG                         ATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAG
genomic: GATGGGATGAAGgtaaaatgaa ... tgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAG
EST: gi|9983220|gb|BE657328.1|BE657328
EST:     TGATGGGATGAAG                         ATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAG
genomic: TGATGGGATGAAGgtaaaatgaa ... tgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacattaggaggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG
                                          tcttgttt  CT-rich tract
                                      tatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgaaaatttgtgttattcgtgctttacacccaataggtaataacattaggaggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG