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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag

Basic information

species Oryza sativa
transcript LOC_Os02g52420.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaatt-ggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag
||| ||||| || ||||||||||| || |  ||||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||||||||   |||||||||       |||    | | ||||||||  |   |||| |  | | | |      
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatccaaaatccagagataaca-------actttgaataaataagaaaacttacaattaattttcatggcag---

upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag
|||||| || || || || ||| |  ||||||| |||||||||||||| || || ||||| ||||| || ||||| ||||| ||||| ||| | ||||| ||    |     || ||      ||   | |||| |||  |    | || ||| ||    |   |  || ||  || |||
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtg---aaaaaaaatttgttgacacat-tctttatttgcag

upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G37040.1 (Arabidopsis thaliana), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaa------ttggagataacacacacat----actgcatacatataagaaagttacaaattgacctcctttgtta-cag
 || |||||||| ||||||||| | ||||| || || ||||| ||||| || |||||||| ||||| || ||||||||||| |||||  | || ||||| ||  ||  |   |||      ||| ||     | ||| ||    |   |   |   || |||  |||  |||  |     |   ||  |||
TTATCCTTCGCCTCTTGGTTATGGAGGTTTCCCGAAAAGTGTTTGCACATCTGTGAATGAATGCATTTGCCATGGTATACCAGATTCAAGACCACTTGAGgtgcgcttttttaaaaggtgtttgtaggggctaaacagatttttatctctgtcccttatgaatcttaataatgtattgtttcctttggcag

upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgt--aagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag-----------------
 |||||||| || || || ||| | || ||||||||||| |||||||| ||||||||||| ||||| || ||||| ||||| ||||| ||||| ||||| ||  |    |   ||      ||||  |     |  | ||     |  | |    |||   || |   |   |   ||| |                  
GTACCCTTCCCCCCTAGGCTATGGTGGATTTCCAAAGAGCGTCTGCACATCAGTGAATGAATGCATTTGCCATGGAATACCAGATTCCCGTCCACTTGAGgtctattttacttaaggacttagatttcttgagc-cagtgtggttaagtcattgtgtttttaagtagtcaaatcacttatacaaaattgtcatttgcag

upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S90_139V6.2 (Physcomitrella patens), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag-----------------------
 || ||||| || ||||||||| |  ||||||||||||| || || ||||| || |||||||||||||||||||| || ||||| || ||||| ||||| ||  |   |   ||||   |  ||   | | | |    |  | |  || |||     | |   ||||     || ||  |                       
TTATCCTTCTCCTCTTGGTTATGGAAGTTTTCCAAAGAGCGTTTGTACCTCTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggt--ttggaaatacaatctagtgctctcttgggtcgaaaacttatgaaccgctctagc-gaccctgggtgatagtgcgaagtcttagtttgctggtcac

upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ35398 (Selaginella moellendorffii), 5'ss of exon 4
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaattggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag
||| || ||||| || || ||  | || ||||| ||||| || ||||| || ||||| || |||||||| || |||||||| ||||||||||| ||| | ||||  ||    || |   |||  |   |   || || |   || |  ||                              
ATATCCATCGCCTCTCGGATACGGTGGGTTTCCGAAGAGCGTGTGCACGTCCGTGAACGAATGCATCTGCCACGGTATACCCGATTCTCGTCCGCTTCAGgtaacacaagttaagtcccagactaagtaagaatcct-cgaccacaccag------------------------------

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|29657569|gb|CB653844.1|CB653844
EST:     CAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAA                         GATGGTGACATTATCCACATTGATGTTACTGTTTATCTCAAT
genomic: CAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatc ... tttgttacagGATGGTGACATTATCAACATTGATGTTACTGTTTATCTCAAT
EST: gi|86494445|gb|CI137078.1|CI137078
EST:     AATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAA                         GATGGTGACATTATCAACATTGATGTTACTGTTTATCTCAAT
genomic: AATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatc ... tttgttacagGATGGTGACATTATCAACATTGATGTTACTGTTTATCTCAAT
EST: gi|29657570|gb|CB653845.1|CB653845
EST:     CAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAA                         GATGGTGACATTATCAACATTGATGTTACTGTTTATCTCAAT
genomic: CAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatc ... tttgttacagGATGGTGACATTATCAACATTGATGTTACTGTTTATCTCAAT