Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTACACGAGTTCCTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttttgtgatcctgatctatcagttaactggttatggttgtgctgtgaaacaagtaaagaaaaatacaattggcctttgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g65450.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65450.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G114172_T01 (Zea mays), 5'ss of exon 4
ATCTACACGAGTTCCTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttttgtgatcctgatctatcagttaactggttatggttgtgctgtgaaac-----aagtaaagaaa-------aatacaattggcctttgaatgcag
|||| ||| |||||||| | ||||||||| || ||||||| ||||||||||||||||||||||||||||| |||||  | ||| ||||||||| ||| || ||||| || || |  || |      | | |||| |        |||||| |||  | ||| ||||||
ATCTTCACCAGTTCCTCACAGCTGCATATGCAAAATATGACATCATGATATGGTCAGCAACTAGgtaagc-ttttggcaccctcatctatcagctaattgtttatgattctgattcgagattgccaaggcaaagtagtagtagtaatacatttgatccttggatgcag
















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|86495698|gb|CI138331.1|CI138331
EST:     TATCATGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: TATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
EST: gi|86495747|gb|CI138380.1|CI138380
EST:     TGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: TGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
EST: gi|29685721|gb|CB681996.1|CB681996
EST:     CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
EST: gi|29676775|gb|CB673050.1|CB673050
EST:     CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
EST: gi|396941533|gb|HO188742.1|HO188742
EST:     CTCTCTGCTGCATATTCAGAATATGATATCCTGATATGGTCAGCAACTAG                         CATGAATTGGGTGGGGATGA
genomic: CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGA
EST: gi|29676776|gb|CB673051.1|CB673051
EST:     CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
EST: gi|29685722|gb|CB681997.1|CB681997
EST:     CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAG                         CATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC
genomic: CTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttt ... ttgaatgcagCATGAAATGGGTGGGGATGAAGATGGACCAACTTGGAGTTCTTGGCAACCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTACACGAGTTCCTCTCTGCTGCATATTCAGAATATGATATCATGATATGGTCAGCAACTAGgtaagcgttttgtgatcctgatctatcagttaactggttatggttgtgctgtgaaacaagtaaagaaaaatacaattggcctttgaatgcag

- - - - - - - - -  TGCTGC