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

TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc...

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 14
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc----
|||||||||||| || |||||||||||||||||||| |||||||||||  ||  ||  ||||| |   | ||| ||||| |  |||||||| ||   |  |    ||        | | |  |     | | |   ||| |      
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatattttatttcttgttgt-ggtcttggttttt-tcattagtgtttct--taacgcgccaagacaatgacagttgtcaatgtgataccttatctttaatat

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc---
|||||||||||| || |||||||||||||||||||| |||||||||||  |||||   ||||| | ||| || || ||| ||||||||||| ||   |  | |  ||  |     | | |  | ||  | | |   ||  |     
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgttctcttgttgt-aatctttatattttttgttagtgtttct--taacgatccaagataatgacagctgtcggcgtgataccctattttgtacc

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 12
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc--
|||||||||||| || ||| ||||| |||||||||| |||||||||||  ||||||  ||||| | |   |   ||||| |  |||||||| ||   |  |    ||     |  | | |  |     | | ||  ||| |    
TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTGgtaatatttgttttcttgttgttatcttgattttttttcattagtgtttct--taacgcgacaagacaacgacagctgtcaatgtgatactttatctttaat

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 12
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc--
||||||||||||||||||||| ||||||||  |||| || ||||||  ||||       || | |  |||     |  | || ||    ||    |||||  | | |     |      |  ||  ||  || | | |||     
TGATCATGAAGGTGGAAATGTTAGTGCTCACGCTGGTCACCTGgtatgtatttgccacatgatcttgatgcatgataatgtt-ttgaacttatagacatt--tctgatggttctgtttttggctaatga-tgtttcttcacttag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttt-tcaatgtt----gatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc
||||||||||||||||||||| |||||||| ||||| || ||||||  |||    |||   | | ||||| ||    ||||   ||   |   ||| ||||   |  |||    ||| |    ||   || |   ||  |        
TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttt----tgctaa-aaattcttgttca-tgtag--------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaatta----ttgtttctttgttttca-----------atgttgatttttcttgt--tagtgttgctaa---cattgttttaacctgccaccggatcactgctggctgctgcatcatcc----------------------------------------------------------------------------
|||||||||||| || |||||||||||||| ||||| ||||| |||| |     | | ||| || |  | |           ||||  | |||| ||||  |   |  | |||   |||| ||||| ||||        | |  |     ||   |||  |                                                                              
TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTAgtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagaggaatgttctctattgactgatattatgctcaattcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 5'ss of exon 11
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc-
||||||||| ||||| ||||| |||||||||||||  ||||||||||  | ||  |       | |  |  |  | | || | | | ||      |   |   |  |  |  | |||      | || |  |||  |  |||  
TGATCATGAGGGTGGCAATGTAAGTGCTCATACTGTGCATCTGgtaagcagtgaattggatcctcctttcattctctgtcctctaaatgcgcaatatgctaaatcgaagttgctccgtcattttacttga-gctttacaatcta

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|3758954|gb|C96653.1|C96653
EST:     TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc

- - - - - GGTGGA