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'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------tctttgtttacctgttatacttgtaatc--tcgattt-tcctattcttattt----ttgtcagcatttagctattagtgt--ggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
                                                                      |  | |  || || || || ||  | ||  |  || | |  || | || ||     || ||| | | |  |||| ||| |   | ||| ||  | |||  ||||||||||| ||||||||||||||||| ||||| ||||||||||||||| || | || || | ||||||||
gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatct-ttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------tctttgtttacctgttatacttgtaatc--tcgattt-tcctattcttattt----ttgtcagcatttagctattagtgt--ggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG------------------------------------
                                                                      |  | |  || || || || ||  | ||  |  || | |  || | || ||     || ||| | | |  |||| ||| |   | ||| ||  | |||  ||||||||||| ||||||||||||||||| ||||| ||||||||||||||| || | || || | ||||||||                                    
gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatct-ttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAGGTATTCTGTGCACACTGCTGTCTGCTTGTGTTATTG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 7
-tctttgtttacctgttatacttgta-atctcgattttcct--attcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
 ||||||| |  |  ||    |  || |||||  ||||||   ||||| |   |  |   |  | || | | ||  ||  ||| |   | ||   |||||| |||| ||||||||||||||||| ||||| ||||||||||||||| || | || || | ||| ||||
atctttgtattgccattcctttaatatatctcagttttccccaattctcaccctattt--ctataagttttaagcttg--ctgtttatttttctcttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTCCCAG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063909_T04 (Zea mays), 3'ss of exon 6
--tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG------------------------------------
  |  |  ||    ||  || | | |||| |   |     |   |  ||| ||  |  | ||  |  | |  | |   |   || |  |||  |||||  |||| ||||||||||| ||||| |||||||||||||| |||||| || | || || | ||| ||||                                    
gcttatctttctattgccattcctttaatatttttcagtgttcgccaattcttcccctctttctgtaagt--tttaagcatgtggggtttttcttgttctagGTCCCAACCAAAGATCAAGTTGATGCTCTATCAAAAGAATTGCTTGCGCGCTCAACTGTCCCAGGTATTTTGATCACACCGCTGGCTACTTGTGTTATTG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 6
--tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
  |  |  ||    ||  || | | |||| |   |     |   |  ||| ||  |  | ||  |  | |  | |   |   || |  |||  |||||  |||| ||||||||||| ||||| |||||||||||||| |||||| || | || || | ||| ||||
gcttatctttctattgccattcctttaatatttttcagtgttcgccaattcttcccctctttctgtaagt--tttaagcatgtggggtttttcttgttctagGTCCCAACCAAAGATCAAGTTGATGCTCTATCAAAAGAATTGCTTGCGCGCTCAACTGTCCCAG

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|117245193|gb|CT843395.1|CT843395
EST:     GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAG                         GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
EST: gi|33793807|gb|CF322790.1|CF322790
EST:     GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAG                         GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTAGACTGGAAAG                         GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
EST: gi|86904765|gb|CI310558.1|CI310558
EST:     GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAG                         GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
                             gactgat  putative branch site (score: 3)
                                             tttgtttc  putative PPT
                                       tatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA