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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT

Basic information

species Oryza sativa
transcript LOC_Os12g30020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 3
tgctttgggagattgtctggacg-gagttatttttcttcctgcaccaggcaatgatttc-cactgggatgctttaatgaa--tggtctgtaattgt---ctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
      || |  || | |   |  |    | ||    |  | ||  | |||| | |||| || |   ||   ||| |  |  || |    |||  |    | | |||||| |||||||| |||||||||||||||||||||| | ||||||| ||||||||| ||| |||||||||||  ||||| |  | ||| | |||||||| |
------ggaaatttatttcttcatgcaccagttcatatgattcaa-aagcaaggttttctcatttacataacttattacagctgatgctcaatcttacattttccagGAAATATATGATAAACAAAAAGAACTTATTTTACTCGGGGAGCGAATTGTACTTGTAACACTTGGGTTTGACCTGAATATTGACCATGCTTACAAGCCCT

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 4
tgctttgggagattgtctggacggagttatttttcttcc-tgcaccaggcaatgatttccactgggat-gctttaatgaatg-----gtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
       |   ||| |||| | | |    ||| | ||   | ||  ||  |   ||||      |  | | || ||   ||      |  |||| |      |||||||| | |||||| ||||||||||||||||||||||||  |||||||||||||||| ||| |||||||||||  | ||| |  | ||| | || ||||| |
-------gtttattttctgcatgcaccagtttctatttggttcaaaagaaagccatttatgtaagagttgtttcaactgatattagtgcttgtactgcctattgcagGAAATCTATGATAAACAAAAAGAACTTATTTTACTTGGAGAGCGAGTTGTACTTGTAACACTTGGGTTTGACCTTAATATTAACCATGCCTATAAGCCCT

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 3
tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtc-tgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
  || ||||   || | |  |   |    || || |      | ||     |  || || ||    |  | || |   |  || || ||||||  |  |||||||| ||||| || || |||||| | ||||||||||  ||| | ||||| |||||||||||||| |||||| |||||||||| ||||| || || ||| 
aactgtggggatttatttcaaaataaaatttcttttgaacttatcaattttttcttacctctcttgtaatatattttcttttcatgcaattgtgac-acagGAAGTGTATGAGCAGCATAAAGAATTAATTTTACTTGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCACCATCCTTATAAACCTC

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 3
tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtc-tgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
|    || |   || | |  |   |    || || |      | ||     |  || || ||    |  | ||     |  || || ||||||  |  ||||| || ||||| || || |||||| | |||||||| |  ||| | ||||| |||||||||||||| |||||| |||||||||||||||| || || ||| 
ttaactgtggatttatttcaaaataaaatttcttttgaacttatcaatttttccttacctctcttgtaatatatgtttttctcatgcaattgtggc-acagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 5
-tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtctgtaatt-gtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
   | |  |   ||||||      |    || | || || ||  |  | ||  | | || | |      |||   || |  |   ||| ||    | |||||||||||||||| ||||||||||| |||||  ||  ||  ||     |||||||| | || || || ||||| || |||||  ||||||| || |||||| 
cctcctatgatcattgtccttgtcgttggatctctcatc-tgtgctggtcaccg-tctctattatttctcttctttgtactgaacgtatttcacttttgcagGAAGTATATGAGCAACAAAAAGAGCTTATACTAAATGGAGAAAAGATTGTACTTTCTACGCTGGGATTTGACTTCAATGTTTATCATCCTTATAAGCCTC

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 3
tgctttgggagattgtctggacggagttatttt----tcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
    |   |  | |   |    |   || |||     |  |  ||        | |  ||||| ||   ||| ||      ||| | |  |  | ||  ||||||| |||||||| || || || ||| | ||||||||||  ||| | ||||||||||| || ||||| |||||| | |||||||| |||||||| || ||  
---ctcaaggaaatacttcattgtcattgtttgaaggtggtggtggtggttttatttttttccccttccatgtttcttcatatgtttttcatctatca-tgcagGAGGTATATGAACAGCAGAAGGAATTAATTTTACTTGGAGAGAGGGTTGTACTTGCTACACTTGGTTTTGATCTTAATGTGCACCATCCATATAAACCCC

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
-----tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
     | |   | | | ||   ||   |  |  |||     |     |        | |||  || |    || |||  | | || || ||  |   |  |||||||||||||||| ||||||||||| || |||||| |||  ||| | ||||||||||||||||| || |||||  | ||||| || || ||||| || ||  
tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttatgtaattatcatt----tgttttggtcattgatcggtg-tccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC

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|58654685|gb|CK043365.1|CK043365
EST:     AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAG                         GAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
genomic: AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAGgtaacaataa ... gtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
EST: gi|33675720|gb|CF303959.1|CF303959
EST:     AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAG                         GAAGTATATGATCAACANAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
genomic: AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAGgtaacaataa ... gtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
EST: gi|58656723|gb|CK045403.1|CK045403
EST:     AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAG                         GAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
genomic: AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAGgtaacaataa ... gtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
EST: gi|29677818|gb|CB674093.1|CB674093
EST:     AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAG                         GAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA
genomic: AGATTATTCATAAAAAGGATCCTGCTGCTGGTCAGAGAATCAAGCAGAAGgtaacaataa ... gtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcaatgatttccactgggatgctttaatgaatggtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
                       ctttaat  putative branch site (score: 4)
                                           ttgtctct  putative PPT
                        tttaatgaat  TA-rich tract