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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT

Basic information

species Oryza sativa
transcript LOC_Os01g62420.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
--tctttatggct--tttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtctttt-ttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
  |  |    |||  ||||   |  |||       || || ||    | ||||| | ||      | |||| |   ||| |  |    ||| |  | |||| |||| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||     
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaattt-----ctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG-----

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
--tctttatggcttttgtggtccattgtactgtgctgacatagaagt-cttctcatttctccacc--cctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
  |    |   || || |  |    | ||      |  |||   |   |||   ||||    | |   |||  |||| |      |||   ||     ||| |||  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| |||     
gttaaaaaaaactgttctaatt-gctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgta----tttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG-----

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| ||||||| 
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGGTATG

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| |||     
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAG-----

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------tctttatggcttttgtggtccatt----gtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
                                                                     | || |||    |  ||  |  ||    | ||| | ||  | |||        |||   | |        | || ||| ||     |||| |  | ||  |     ||||   | |  |  | ||| | ||||||||  | || ||||||||||| ||||||||||||||||| ||||| || | ||| || || ||||| ||      
gtatgtatattgtcaaacatttaatctctttttgctatctcagttcgttctcgtttacagtgagacctgttttgatgatagtgatgcccgtttctacgcactatactcccttagtgtgtgattcaaaccccacagaaatatttgttggctaaaaaactctttttgttggtaatggcagATCGGGTGACAAACTGGTCAAATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGAA-----

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtct-tctcatttctccacccctaactttt-tgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
 ||  |||  |||     |      ||      |    |||  || | | |  | | |  ||   ||  |||  ||  |  ||| ||  |  | | ||||||| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| |||||      
-ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgct-attttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA-----

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ31929 (Selaginella moellendorffii), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
                               | |    |   | | || | || | | || ||  | ||     ||     ||||  |    | |  |||| ||| |    || ||||  ||||| ||  | ||||| || ||||| ||||| |||||||| || || ||||| |||||||| ||||||||||||||   
-------------------------------gtttgggtttca-tgtttttatct-tgcatccaaagctcacactcaagcatacttcttgattgtggcagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCTCAGGAGGTCCA

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|33693438|gb|CF321677.1|CF321677
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692149|gb|CF320388.1|CF320388
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33694018|gb|CF322257.1|CF322257
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689964|gb|CF318203.1|CF318203
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
EST: gi|33828594|gb|CF340117.1|CF340117
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCANACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33827559|gb|CF339596.1|CF339596
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692177|gb|CF320416.1|CF320416
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692251|gb|CF320490.1|CF320490
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33685938|gb|CF314177.1|CF314177
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTAGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689283|gb|CF317522.1|CF317522
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
EST: gi|33687151|gb|CF315390.1|CF315390
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGGTTGTTTTGGCATATGAACCAGTTTGG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATG-TTGTTTTGGCATATGAACCAGTTTGG
EST: gi|33685460|gb|CF313699.1|CF313699
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58679577|gb|CK068264.1|CK068264
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58683989|gb|CK072676.1|CK072676
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAG
EST: gi|33692942|gb|CF321181.1|CF321181
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33828383|gb|CF340010.1|CF340010
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCANACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33691808|gb|CF320047.1|CF320047
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGAC
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGAC
EST: gi|58669404|gb|CK058090.1|CK058090
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689638|gb|CF317877.1|CF317877
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCATACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACC
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACC
EST: gi|58674808|gb|CK063495.1|CK063495
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33693863|gb|CF322102.1|CF322102
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33685357|gb|CF313596.1|CF313596
EST:     GCAGGAACAACGATGGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAACGATGG-AAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33801873|gb|CF326808.1|CF326808
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692386|gb|CF320625.1|CF320625
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
EST: gi|33691552|gb|CF319791.1|CF319791
EST:     GCAGGAACAACCGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGAC
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGAC
EST: gi|33690870|gb|CF319109.1|CF319109
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT
                ccctaac  putative branch site (score: 2)
                                             tatttttc  putative PPT
                       tttttgtctttttta  TA-rich tract