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

gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA

Basic information

species Oryza sativa
transcript LOC_Os11g03730.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 9
gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaata--tcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
|||||  ||  || || | ||| |||||  | | ||   | |  || || ||  ||    |    | |   |||  |||||||| ||||| |||||||||||||||||||  || ||||| ||||||||||| 
gtaattgttttcagatctgttaaatctt--ttatcaacacggggcttctaaactgatggaatttccctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 9
gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaata--tcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
|||||  ||  || |||| ||| |||||  | | ||   | |  || || ||  ||    |      |   |||  |||||||| ||||| |||||||||||||||||||  || ||||| ||||||||||| 
gtaattgttttcagatttgttaaatctt--ttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 9
gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactct---ttaaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
|||||  ||  ||  ||| ||| ||| |  |   ||| | || | || |  || ||||  ||  ||    ||  |  |||||| ||||||| ||||||||||||||||||| ||| ||||||||||||||||| 
gtaattgttttcaggtttgttaaatcat--ttgtcactgttggcttctt--attgacagaaagttccctcttgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 9
----------------------gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaata--tcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
                      |||||  ||  || |||| ||| |||||  | | ||   | |  || || ||  ||    |      |   |||  |||||||| ||||| |||||||||||||||||||  || ||||| ||||||||||| 
ccaatatgggtattcaacaatggtaattgttttcagatttgttaaatctt--ttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG

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|29672785|gb|CB669060.1|CB669060
EST:     CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG                         GAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA
genomic: CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATGgtaataattg ... taaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA
EST: gi|29644765|gb|CB649772.1|CB649772
EST:     CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG                         GAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA
genomic: CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATGgtaataattg ... taaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA
EST: gi|29646541|gb|CB651548.1|CB651548
EST:     CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTNCA-CAATG                         GAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTA
genomic: CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTT-CAACAATGgtaataattg ... taaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTA
EST: gi|29636288|gb|CB641297.1|CB641297
EST:     CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG                         GAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA
genomic: CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATGgtaataattg ... taaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgatcaccacagctgacctcctgaatcgacactaaactctttaaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
                                 cactaaa  putative branch site (score: 2)
                                        ctcttt  CT-rich tract
                                    taaactctttaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC