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

...ttttctcctggagcaactgcttgtgtttaagctttaaaaaaaagtttcattaaatttcactattctttgcccatactaaataaggttctttatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 11
ttttctcctggagcaactgcttgtgtttaagctttaaaaaaaagtttcattaaatttcactattctttgcccatactaa-----ataaggttctttatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG
  |        |||| |  |||   | |  ||||    |    ||| | |      | | | |||||  |  | |  ||     | | |  | |  |   |  || | ||| | ||||| |||||||| |||||||||||||||||||| |||||||| || ||||| || |||  |||||||
-ctcaattacaagcatcaccttaaatatgtgctt----agttggttgcgtgttgcgttagtcttcttaacttaaaagaactgtaacacgagtgtacaaaatacagGTTACAGTATCTAAGGATGACACAGTCATCCTTGATGGAGCTGGAGATAAGAAGGCCATTGAAGAGAGAGCTGAGCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------ttttctcctggagcaactgcttgtgtttaagctttaaaaaaaagtttcattaaatttcactattctttgcccatactaaataaggttcttta---tgttt---tagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG
                       | |   | ||| |   ||   | ||    || |||    |  |  |||     || ||  | ||   |    |   ||  | ||  |  |     | |||   ||| | ||| | || || || |||||||| || |||||||| ||||| || ||||||| |||||||||||||||||| |||
gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattctcagcatatccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG
















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|19053143|gb|BM731810.1|BM731810
EST:     GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAG                         ATAACAATTTCTAAAGATGACACTGTCATCCTTGAT
genomic: GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAGgtaaccattt ... tatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGAT
EST: gi|24205139|gb|BU964392.1|BU964392
EST:     GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAG                         ATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG
genomic: GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAGgtaaccattt ... tatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG
EST: gi|16284788|gb|BI946271.1|BI946271
EST:     GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAG                         ATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG
genomic: GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAGgtaaccattt ... tatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG
EST: gi|16278620|gb|BI942998.1|BI942998
EST:     GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAG                         ATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG
genomic: GTTTGAATCTTGAAAAAGTAGACCTGGACTTATTTGGCTCTTGCAAGAAGgtaaccattt ... tatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattaaatttcactattctttgcccatactaaataaggttctttatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG
                            tactaaa  putative branch site (score: 1)
                                        ttctttat  putative PPT
     taaatttcactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctcctggagcaactgcttgtgtttaagctttaaaaaaaagtttcattaaatttcactattctttgcccatactaaataaggttctttatgttttagATAACAATTTCTAAAGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- -tctcctg
- - - - - - -caactgc
- - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatac