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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGACATGATTGCTGTGAGTAATATGCGTTGCTTATGTGGCCCTGACACCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaatattgctttctttttggttctttctgaacatttatctgctaccaacctgatctcatgatgtattaattgattcctactgataacag

Basic information

species Oryza sativa
transcript LOC_Os02g25580.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G052880_T01 (Zea mays), 5'ss of exon 16
TGATGACATGATTGCTGTGAGTAATATGCGTTGCTTATGTGGCCCTGACACCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaatattgctttctttttggttctttctgaacatttatctgctaccaacctgatctcatgatgtattaattgattcctactgataacag
|||||||||||||||||| | ||||||||||||||||||||| ||||| ||||||||||| || | ||| ||||||||  | ||||||||||||||||||||||||    ||  | | | | || | |||| | |  | |||||         | |  ||||| | ||||||||  ||  |||||  |||||||||
TGATGACATGATTGCTGTAAATAATATGCGTTGCTTATGTGGGCCTGATACCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattgtag-gttatttcttggcttctatttctatattta---------atctggatctgaagatgtattcttttcttcctgttgataacag
















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|29626795|gb|CB631806.1|CB631806
EST:     CCAAAAAGTCCTCGGGAGGAGGTTTTACGCTTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|38481465|gb|CF965554.1|CF965554
EST:     CCAAAAAGTCCTCGGGAGGAGGTTTTACGCTTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|218485563|gb|FG949368.1|FG949368
EST:     CCAAAAAGTCCTCGGGAGGAGGTTTTACGCTTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|29626796|gb|CB631807.1|CB631807
EST:     TTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: TTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|29689435|gb|CB685710.1|CB685710
EST:     CCAAAAAGTCCTCGGGAGGAGGTTTTACGTCTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|86831700|gb|CI301550.1|CI301550
EST:     CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
EST: gi|66914840|gb|CX101688.1|CX101688
EST:     CCAAAAAGTCCTCAGGAGGAGGTTTTACGCTTAAATTTGATGTTCACAAG                         AAGAAGCATGGACTTAAAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA
genomic: CCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaa ... ctgataacagAAGAAGCATGGACTTAGAAAGGAGCGAACTGGGGAAGAATCTACATGGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGACATGATTGCTGTGAGTAATATGCGTTGCTTATGTGGCCCTGACACCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaatattgctttctttttggttctttctgaacatttatctgctaccaacctgatctcatgatgtattaattgattcctactgataacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG