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

gtgtgtctatagattcgattaattgtgttttaactaggaatgtacacttgcttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGGGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 5
gtgtgtctatagattcgattaattgtgtttt-aactaggaatgtacacttgcttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGGGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG
                       |||||||| |||||   |  |  |  |   ||||   ||    | ||| |||    |  || || ||||| |    || ||||||||||||||||| ||| | ||||||||||||||||||||||| |||||||| |||||||| ||  | || ||||||||||| ||||||||||||||||||
----------------------gtgtgttttgaactatttagttgtaact-tgtaagtgtac----actgttatcttttgtgaaactgacacacgggc-atatgcagTGCAACAGCTCAAGATATCCGCACAATGATTATTGGCCGATTGCTTGCTGGAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 5
gtgtgtctatagattcgattaattgtgtttt-aactaggaatgtaca-cttgcttaagaaaaccgctattgt-catccaacgga-aacctaacacatgaaagatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGGGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG
                       |||||||| |||||   |  | || ||||       | || | |||  |  ||  ||| || |  || |||||   || || || || ||||||||||| ||| | ||||| ||||||||||| || || |||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||||
----------------------gtgtgttttgaactatttagttgcaacttgtaagtatacactgttatcttatatgaaactgacagtctgacaca---aatatctgtagCGCAACAGCTCAAGATATCCGCACCATGATTATTGGTCGGTTGCTTGCTGGAATTGGTATTGGGATCTCATCTGCACTTGTACCCCTTTACATATCTGAG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgtctatagattcgattaattgtgttttaactaggaatgtacacttgcttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGGGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG
    |||| |  ||| | |   | |    | |  |   ||| |    ||   | | | ||  |  | |   ||  |    ||||| ||   |||     ||| |||||| ||||| ||   ||| |  || ||||| |||||  | ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||||
----gtctgtc-atttgtt--gtagaccataagatcataatctttgtttatatcaaataaaagaaaat---atttataataaacccaa-gtatgttcacttttcagTGCGACAGCACAGAGTGTGCAGACTATGATAATTGGTAGGTTACTTGCTGGCATTGGAATTGGCATCTCATCTGCACTTGTGCCACTTTACATATCTGAG

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagaaaaccgctattgtcatccaacggaaacctaacacatgaaagatttgcagTGCAACAGCTCATGATGTTCGCACAATGATTATTGGCCGATTACTTGCTGGGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG
                               acctaac  putative branch site (score: 2)
                                           aaagattt  TA-rich tract