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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcattgtatataaacaatatttgcataaactagagaacacctgaatgtctgccattggcatgaagattcactgtattttcaacttttcacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGTCCTGAGTTCTCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTA

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13790.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 4
-gcttcattgta-tataaacaatatttgcataaactagagaac--acctgaatgtctgccattggcatgaagattcactgtattttcaacttttcacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGTCCTGAGTTCTCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTA
   ||  ||| | ||| | |  ||| |   || | |  ||     |  |   ||| |   | |   ||| | |   | |  ||  |  |  |  ||   |||||||||| ||||| || |||||||||||||||||||||||||| ||  | ||||||  |||||| || ||||||||||| |||||||| |||||||||||||
tcttttcttgcaatattagcc-tatcttattatattgaagttttaattttgttgtatatgaatctaatgtaaaaagattcaatgctttatgtgcca---tacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA

upper sequence: LOC_Os03g13790.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 4
gcttcattgtatataaacaatatttgcataaactagagaac----acctgaatgtctgccattggcatgaagattcactgtattttcaacttttcacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGTCCTGAGTTCTCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTA
| || ||  | | |   |||  || || ||   ||   ||     |      ||| |  || |   ||  | | | | |  ||  |  |  |  ||   |||||||||| ||||| || |||||||||||||| ||||||||||| || || ||||||  |||||| || ||||||||||| |||||||| |||||||||||||
gtttaatcttttcttg-caacgttagcctaccttattaaagtttaattctgttgtatatcaatctaatataaaatgatttaatgctttatgtgcca---tacagGTCAGGCATTACTATTATCGTCTTGTTCGGCGCATGAAGAAGCTACTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA
















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|88362353|gb|CI608744.1|CI608744
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCAT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCAT
EST: gi|88328977|gb|CI658625.1|CI658625
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTC
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTC
EST: gi|117217875|gb|CT845173.1|CT845173
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|29628330|gb|CB633341.1|CB633341
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88373410|gb|CI614746.1|CI614746
EST:     AATTTTGAGAAGATTACGCTGGGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTAATATCGTCTTGTTCGAAGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88351778|gb|CI617503.1|CI617503
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|58689184|gb|CK077871.1|CK077871
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88409790|gb|CI571047.1|CI571047
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88730127|gb|CI753742.1|CI753742
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTA
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTA
EST: gi|88351022|gb|CI620682.1|CI620682
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88352611|gb|CI624550.1|CI624550
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|29621639|gb|CB626650.1|CB626650
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|29630702|gb|CB635711.1|CB635711
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|86904162|gb|CI304596.1|CI304596
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88344650|gb|CI637259.1|CI637259
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCA
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCA
EST: gi|58612137|gb|CK039849.1|CK039849
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|58666001|gb|CK054687.1|CK054687
EST:     ATTTTGAGAAGATTACGCTGCGTGT-CAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: ATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88387482|gb|CI583000.1|CI583000
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|87023602|gb|CI286353.1|CI286353
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|29618831|gb|CB623843.1|CB623843
EST:     TACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: TACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88573702|gb|CI665471.1|CI665471
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCA
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCA
EST: gi|88450057|gb|CI572188.1|CI572188
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88337044|gb|CI628130.1|CI628130
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|29617184|gb|CB622196.1|CB622196
EST:     AGAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATAGAAGAAACTTCTCGG
genomic: AGAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCAT-GAAGAAACTTCTCGG
EST: gi|88412252|gb|CI573528.1|CI573528
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
EST: gi|88370989|gb|CI595101.1|CI595101
EST:     AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG                         GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT
genomic: AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAGgtacaccatc ... cacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtctgccattggcatgaagattcactgtattttcaacttttcacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGTCCTGAGTTCTCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTA
                                        cttttcac  CT-rich tract
                               tattttcaactttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttcattgtatataaacaatatttgcataaactagagaacacctgaatgtctgccattggcatgaagattcactgtattttcaacttttcacattacagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTCGGTCCTGAGTTCTCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
gcttcat
- - - - - - - -aacaata
- - - - - - - - - - - -ttgcata
- - - - - - - - - - - - - - - - - - - - cacctga
- - - - - - - - - - - - - - - - - - - - - - - - tgtctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcactg