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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctttttgatggaaaccaagcatttcattcagcatctgcaaagtgctgacttgggtgatgatgtgttttgtaag

Basic information

species Oryza sativa
transcript LOC_Os05g46430.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46430.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G394827_T03 (Zea mays), 5'ss of exon 2
AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctt-tttgatggaaac-caagcatttcattcagcatctgcaaagtgctgact-tgggtgatgatgtgttttgtaag---------------------
|||| |||||| |||||||||||||| ||  ||||||||||||||||||||||||||||||| |||||||| |||||  ||||||||| ||| ||||| |||     || || || | |||  || |||| || | | || |      |    |  ||      ||||    | |    |   |   ||    |||| ||  |                        
AACTCCTTCCTTGTGAAGCAGTTCGGCAACGGCAATGCCAAGGTGCAGTTCACCAAGGAGCCGAACAACCTCTACAACATCCACTCCTTCAAACACTCGGgtat---gttgcgtccttcaaagtttctggattgtctaattgtcgtgtatatgtaacacctgtgatcttagtaataaaaataataaatggctttgtgcttactgctctggctgttttgttctgttag

upper sequence: LOC_Os05g46430.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G088060_T04 (Zea mays), 5'ss of exon 2
AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctttttgatggaaaccaagcatttcat-tcagcatctgcaaagtgctgacttgggtgatgatgtgttttgtaag--------------
|||| |||||||||||||||||| || ||  |||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||| ||||||||  |  |         |   |     ||   |    |  ||| |     || | || | || |      ||    ||| || | || |||   ||||||   |              
AACTCCTTCCTGGTGAAGCAGTTTGGCAACGGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTCTACAATGTACACTCCTACAAGTACTCTGgtatgctgctctcctcagtttctggattgatctgcctacagaa-caccttatgtgatcttagtaataaacaataaatgattttg-tgttgac-cgttttgcctgtttttttgtttcag

upper sequence: LOC_Os05g46430.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g02560.t01 (Vitis vinifera), 5'ss of exon 2
AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctttttgatggaaaccaagcatttcattcagcatctgcaaagtgctgacttgggtga--tgatgtgttttgtaag-
  || ||| || |||||| ||||||||||  |||  ||||  |||||||||| ||| |||  |||||| || ||||| ||| |||||||||||||||||||| | |||||| |  |   | |||| |    | |  ||     |           |||  |  | |  |   || ||  | | | |   ||||||  || ||    
TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgt-attagtcgatcat---accattacc--ttctgggaaaattattttatggcaaattgggttttttgatcttgttggttagagcgggttgatgtcattggtttcc

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|88732655|gb|CI755832.1|CI755832
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88954777|gb|CI720226.1|CI720226
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|2311591|gb|C27746.1|C27746
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTNACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|87017330|gb|CI301366.1|CI301366
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88387591|gb|CI585294.1|CI585294
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88668824|gb|CI719781.1|CI719781
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|66912719|gb|CX099567.1|CX099567
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCG-GAAAGGAC
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAA-GGAC
EST: gi|88351558|gb|CI628778.1|CI628778
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|7168830|gb|AU065482.2|AU065482
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88693410|gb|CI736985.1|CI736985
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88671259|gb|CI723179.1|CI723179
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88335297|gb|CI650262.1|CI650262
EST:     CACCAAGGAGCCCACCAACCTGTACAATGTNCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88717008|gb|CI740518.1|CI740518
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88669327|gb|CI719465.1|CI719465
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88403125|gb|CI570866.1|CI570866
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|86831708|gb|CI301558.1|CI301558
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88670581|gb|CI724697.1|CI724697
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88729856|gb|CI753077.1|CI753077
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88569753|gb|CI660928.1|CI660928
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88337233|gb|CI629523.1|CI629523
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88765644|gb|CI774738.1|CI774738
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88763296|gb|CI772757.1|CI772757
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|86901100|gb|CI306289.1|CI306289
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|89173144|gb|CI720974.1|CI720974
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88354676|gb|CI629108.1|CI629108
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88329547|gb|CI648610.1|CI648610
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88336222|gb|CI647416.1|CI647416
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88345220|gb|CI628474.1|CI628474
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88570868|gb|CI662241.1|CI662241
EST:     ACCAAGGAGCCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: ACCAAGGAG-CCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
EST: gi|88337281|gb|CI629571.1|CI629571
EST:     CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTG                         GCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG
genomic: CACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtc ... gttttgtaagGCTTGGCGAACAAGAAGACCGTGACGATCCAGCCATCAGGCGTGAAGGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctttttgatggaaaccaagcatttcattcagcatctgcaaagtgctgacttgggtgatgatgtgttttgtaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG