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

TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattacccataatctccttgtcaacatttcctgttcattattgagcaatcagctgcttgctaacgaaataaagtttggttccag

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G096585_T02 (Zea mays), 5'ss of exon 4
TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc-ataatct-ccttgtcaacatttcctgttcattattgagca-atcagctgcttgctaacgaa-ataaagtttggttccag-----
||||||||||||| || || || ||||| |||||| |||| ||||||||||| | ||| |||||||| ||||||||| |    |  ||  |||  |||  ||   | | |||   ||| ||| ||  ||| | || || ||||| |   ||  |   || | |       
TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAagatggtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaactactgtattgccaggctacttttgtc

upper sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 4
TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc-ataatct-ccttgtcaacatttcctgttcattattgagca-atcagctgcttgctaacgaaataaagtttggttccag
||||||||||||| || || || ||||| |||||| |||| ||||||||||| | ||| |||||||| ||||||||| |    |  ||  |||  |||  ||   | | |||   ||| ||| ||  ||| | || || ||||| |       | |  | ||||
TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaactac------tgtattgccag
















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|58656111|gb|CK044791.1|CK044791
EST:     TGGTACTGTTATATCAGGGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|58677816|gb|CK066503.1|CK066503
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|218486102|gb|FG952697.1|FG952697
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|4880950|gb|AU065249.1|AU065249
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29624443|gb|CB629454.1|CB629454
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCA
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCA
EST: gi|29675035|gb|CB671310.1|CB671310
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29666721|gb|CB662996.1|CB662996
EST:     TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGTAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29626371|gb|CB631382.1|CB631382
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     TGGTACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATG                         GTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG
genomic: TGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc ... ttggttccagGTTTCTTCTGCCCTGCGCTGGCGAAAGCTGTCAAAACCATGAAAAAAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattacccataatctccttgtcaacatttcctgttcattattgagcaatcagctgcttgctaacgaaataaagtttggttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG