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

CAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctatagattcgattaattgtgttttaactaggaatgtacacttgcttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g04190.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G098011_T02 (Zea mays), 5'ss of exon 5
CAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctatagattcgattaattgtgttttaactaggaatgtacacttgcttaagaaaaccgctattgt-catccaacgga-aacctaacacatgaaagatttgcag
||  |||||| ||||| || ||  |||| || || |||||||| || ||| | || |||||||||||||||  ||| || ||||||||||||||| ||||||||||       || ||   |||  |||  |||| | || ||| ||            || | |||  |  ||  ||| || |  || |||||   || || || ||
CACTAGGTTCCTTTACCGGGGGATCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGATGCAGCCCCACTGGCTGTAGGTGCATTCTTGAGgtgtgt-------tttgaactatttagttgcaacttgtaa-gtatac------------actgttatcttatatgaaactgacagtctgacaca---aatatctgtag

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G153704_T03 (Zea mays), 5'ss of exon 5
CAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctatagattcgattaattgtgttttaactaggaatgtacacttgcttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcag
||  ||||||||||||||| ||| |||| || || |||||||| || ||| | || ||||||||||||||| |||| || ||| ||||||||||| ||||||||||       || ||   |||  ||| ||||| | || ||  ||                  | ||| |||    |  || || ||||| |    || |||||
CACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGATGCAGTCCCACTTGCTCTAGGTGCATTCTTGAGgtgtgt-------tttgaactatttagttgtaacttgtaa-gtgtac------------------actgttatcttttgtgaaactgacacacgggc-atatgcag

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 5'ss of exon 5
CAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctatagattcgattaattgtgttttaactaggaatgtac-acttgcttaagaaaaccg--ctattgtcatccaacggaaacctaacacatgaaagatttgcag
| | |||||| || ||||||||||| |||||||||||||||||||||||| | || ||     ||||||| ||||| || ||  | || || ||| |  |||   | |  |    | |     |   | ||    ||   |  |    || |||||   |   |  || || | ||  |   |                          
CGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGATGCTATCCCGCTTGCCATTGGAGCTTTCTTATGgtaaattttcaagcactaagccatacctattggtgagacgttaattgatttcttaacgcattggttctttttttattgattag--------------------------

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|88385512|gb|CI564172.1|CI564172
EST:     CNGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAAGTGCATTCCTGAG                         TGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG
genomic: CGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctat ... agatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG
EST: gi|66924477|gb|CX111325.1|CX111325
EST:     AATCCCTCTCGCTGTAGGTGCATTCCTGAG                         TGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG
genomic: AATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctat ... agatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG
EST: gi|300215629|gb|HO088255.1|HO088255
EST:     CGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAG                         TGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG
genomic: CGGACGTTCATCCTGGATGCAATCCCTCTCGCTGTAGGTGCATTCCTGAGgtgtgtctat ... agatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGG