Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGGCTTTTAAGAGGTCTGAAGCTTGTGTCGTGGGAAAAGGTGGATGTCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctctttgcccgtctaagccttgttcttttatatgctgtgtacaaacagagtcgatattatttactcgtagttttcttttaacttagcaaccagtttctgtttgttgacatagcgctgagattaacgcatgcttataaatgaaatttggacag

Basic information

species Oryza sativa
transcript LOC_Os02g43850.5
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43850.5 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G130432_T04 (Zea mays), 5'ss of exon 9
AACGGCTTTTAAGAGGTCTGAAGCTTGTGTCGTGGGAAAAGGTGGATGTCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctctttgcccgtctaagccttgttcttttatatgctgt-gtacaaacagagtcgatattatttactcgtagttttctttt----aacttagcaaccagtttct----gtttgttgacatagcgctgagattaacgcatgcttataaatgaaatttggacag
|||  ||||||  ||| || ||||  || || ||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||||||||  | ||  || ||   |    ||||| | | || | |  ||| ||   |  ||   |  |  | ||     |||   | |    || |||||  ||||    |    ||||||  |       ||||| || | || || ||   ||||||||||  ||||
AACACCTTTTACAAGGACTTAAGCGCGTTTCATGGGAAAAGGTGGATGTTAGTTTCCACAATAGTAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtattgcctttgcc-tccgggtggcgttctctcacattcagaagtaaaatttgcttcaccaccaagtgctaactctttctctgtcaacaatttagccgccagcacataaatgtttgtgaaagatatactgaggttgaagcctgttttgtaatgaaattttaacag

upper sequence: LOC_Os02g43850.5 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G834595_T01 (Zea mays), 5'ss of exon 1
--AACGGCTTTTAAGAGGTCTGAAGCTTGTGTCGTGGGAAAAGGTGGATGTCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctctttgcccgtctaagccttgttcttttatatgctgt-gtacaaacagagtcgatattatttactcgtagttttctttt----aacttagcaac--cagtttct----gtttgttgacatagcgctgagattaacgcatgcttataaatgaaatttggacag
  |||  ||||||  ||| || ||||  || || ||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||||||||  | ||  || ||   |    ||||| | |||| | |  ||| ||   |  ||   |  |  | ||     ||| | | |    || ||||| ||  |||    |    ||||||  |       ||||| || | || || ||   ||||||||||  ||||
AGAACACCTTTTACAAGGACTTAAGCGCGTTTCATGGGAAAAGGTGGATGTTAGTTTCCACAACAGTAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtattgcctttgcc-tccgggtggcgttctctcatattcagaagtaaaatttgcttcaccaccaagtgctgactctttccctgtcaacaatttagccacaccagcacataaatgtttgtgaaagatatactgaggttgaagcctgttttgtaatgaaattttaacag
















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|29661652|gb|CB657927.1|CB657927
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|86868479|gb|CI343051.1|CI343051
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88366919|gb|CI553809.1|CI553809
EST:     TCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88224978|gb|CI224894.1|CI224894
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|86879424|gb|CI327127.1|CI327127
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATATCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|117231984|gb|CT853905.1|CT853905
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88251516|gb|CI349944.1|CI349944
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|157651463|gb|EX451097.1|EX451097
EST:     TCAGCTTCCACAACAGTAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|29661620|gb|CB657895.1|CB657895
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|86882806|gb|CI327408.1|CI327408
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCCTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88437330|gb|CI528689.1|CI528689
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|86536794|gb|CI177000.1|CI177000
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|29679608|gb|CB675883.1|CB675883
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88843279|gb|CI372179.1|CI372179
EST:     CAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: CAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88286586|gb|CI517697.1|CI517697
EST:     CAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: CAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88401692|gb|CI588633.1|CI588633
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|33694141|gb|CF322380.1|CF322380
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|29675641|gb|CB671916.1|CB671916
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|31818607|gb|CD645578.1|CD645578
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
EST: gi|88529156|gb|CI456640.1|CI456640
EST:     TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAG                         GTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG
genomic: TCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctcttt ... atttggacagGTCAAAGATCCCGTTATGCATAGCGAAGGTGCCGATGTCATAAACCATATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGGCTTTTAAGAGGTCTGAAGCTTGTGTCGTGGGAAAAGGTGGATGTCAGCTTCCACAACAGCAAAGTAAGATCTGCAGCACATAGTGTGATTCAGgtatctctttgcccgtctaagccttgttcttttatatgctgtgtacaaacagagtcgatattatttactcgtagttttcttttaacttagcaaccagtttctgtttgttgacatagcgctgagattaacgcatgcttataaatgaaatttggacag

- - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG