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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g42410.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 11
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcata-tgtactgtatctt--ctttgcag
|  |||||||||||||||| |||||||| || ||||||||||| |||||||||||| | |||||||| || || ||||||||| |||| || |||||||||||   | ||||| ||| ||| | |  ||||  |   |     | | |     |    |||| || ||   || |   |  ||||||||
CGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTCAACATGGGATTGGTGCGGAAATATGgtcggccactctccctccctccctccttcccaatgtataa---tgtatagtctgcgtctctcgtaatgggttgaaatgtgcctttgcag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 12
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtactgtatcttctttgcag--
|| | ||| || | || |||||| | || || ||||||||||||||  |||| ||  |||||||||| ||||| || ||||| |||||||||||||| ||||  |||||| |   |   | |   | |   |     |  ||  |||  | ||   | |   ||||  ||  ||||  |   |||||   
CACTTGATCGATCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtg-tgtacttctcttgcacag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgcag--
|  | ||| || | || |||||||| || || ||||||||||||||  |||| ||  |||||||||| ||||| || ||||| |||||||||||||| ||||  |||||| |   |   | |   | ||  |   | |  ||  |||  | ||   | |   |||||||    ||||  |   |||||   
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA14G02380.1 (Glycine max), 5'ss of exon 12
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtactgtatcttctttgcag--
|  | ||| |  | || |||||| | || || ||||||||||||||  |||| ||  |||||||||| ||||| || ||||| |||||||||||||| ||||  |||||| |   |   | |   | |   |     |  ||  |||  | ||   | |   ||||  ||  ||||  |   |||||   
CGCTTGATCGGTCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttgcattaatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtg-tgtacttctcttgcacag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 13
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgc-----tctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcag--------
|  | ||  |||| || |||||||| ||||| |||||||| |  |||||||||||  |||||||||| || ||||||||||| ||  | || ||||| ||||  |  ||  |  ||   |          |||   | || |  |   | | | | |  ||  |   | | | | |  |  || |  | |         
CGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCACAACATGGAGTCTGTGCAGAAATTTGgttaacttcaattccttaattcaatagagatcttattatcacctggattgtataatagttt--taaaacacggattaaactttttccgtaatggatcag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 12
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctc----tctctcgctctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcag-------------------
|  | || ||| |  | |||||||| ||||| |||||||| | |||| |||| ||  ||||||| || || || |||||||| ||||||||||| || ||||     ||| | || |    ||| | ||     |        | |    |||        | ||| | |  |  |||| ||  || ||                    
CCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTCAACATGGTGTTGGCGCTGAGATCTGgttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaa--gtatttttcttacaacgtgtctgaatttctgcag

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|89183612|gb|CI046177.1|CI046177
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCA
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCA
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATG                         CATGTCTGTTGTAGAGGACAGCTTTGA
genomic: GTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctct ... ttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCACAACATGGGGTTGGCGCTGAAATATGgtccatctctctctctctctctcgctctccctctccctcgctctctgtgacaagttgttctcatatgtactgtatcttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG