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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g62420.5
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
--tctttatggct--tttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtctttt-ttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
  |  |    |||  ||||   |  |||       || || ||    | ||||| | ||      | |||| |   ||| |  |    ||| |  | |||| |||| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatt-----tctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
--tctttatggcttttgtggtccattgtactgtgctgacatagaagt-cttctcatttctccacc--cctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
  |    |   || || |  |   ||  || |   |  |||   |   |||   ||||    | |   |||  |||| |      |||   ||     ||| |||  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| |||
gttaaaaaaaactgttctaattgctttaacag-attatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgta----tttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG-----
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| |||     
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGGTATG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| |||
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------tctttatggcttttgtggtccatt----gtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
                                                                     | || |||    |  ||  |  ||    | ||| | ||  | |||        |||   | |        | || ||| ||     |||| |  | ||  |     ||||   | |  |  | ||| | ||||||||  | || ||||||||||| ||||||||||||||||| ||||| || | ||| || || ||||| || 
gtatgtatattgtcaaacatttaatctctttttgctatctcagttcgttctcgtttacagtgagacctgttttgatgatagtgatgcccgtttctacgcactatactcccttagtgtgtgattcaaaccccacagaaatatttgttggctaaaaaactctttttgttggtaatggcagATCGGGTGACAAACTGGTCAAATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGAA

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtct-tctcatttctccacccctaactttt-tgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
 ||  |||  |||     |      ||      |    |||  || | | |  | | |  ||   ||  |||  ||  |  ||| ||  |  | | ||||||| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| 
-ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgct-attttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ31929 (Selaginella moellendorffii), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG-----
                               | |    |   | | || | || | | || ||  | ||     ||     ||||  |    | |  |||| ||| |    || ||||  ||||| ||  | ||||| || ||||| ||||| |||||||| || || ||||| |||||||| ||||||||||||     
-------------------------------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|27576926|gb|CA999620.1|CA999620
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33687908|gb|CF316147.1|CF316147
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33691626|gb|CF319865.1|CF319865
EST:     GCAGGAACAACNGATTGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATTATGAACCAGTTTGG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCAT-ATGAACCAGTTTGG
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTAGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGC--ATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     GCAGGAACAACGATGTGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAACGATG-GAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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