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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA

Basic information

species Oryza sativa
transcript LOC_Os02g05630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 3
gtatg---gcattaataattcatgcattacggagcaaaaataattgta-gccaacctaaaaggtggttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA
|||||     | |||  ||| | |  ||  |      | |      || |     ||  |       |    ||| | | |  ||||  |||||||||||| |||||||  ||||||||||||||||||||||| || || | ||| ||| | |||||||||||||||||||||||||||||| ||||||| ||
gtatgctcatactaactattgaggacttttgacttctacactgacatatgatggtcttgatatc--ctcccgtttttttttttttttgctgcagCTGAAACTTACAACCGCACAGATTCAGAATTTCTGAAAGCTGATAGCACTCAAACTCGAGATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGA

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 2
gtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgc---agCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA
|||      || ||  | |   |||   ||      |    |  |   |    | | |||| |  ||||  |  |||| | || ||||   ||| ||||| |||||||  ||||||||||||||||||||||| || ||  |||| ||| | |||||||||||||||||||||||||||||| ||||||| ||
gtactttcatattagcttaactattgtagacttttgacttgtacactgag---atatggtgatcttgatacccttgtattatttttgctgcagCCGAAACTTACAACCTCACAGATTCAGAATTTCTGAAAGCTGATAGCTGTCAAACTCGAGATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGA

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggcattaataattcatgcattacggagcaaaaataattgtagcc---aacctaaaaggtggttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA
|| |    | |||  ||| |    |  |||   |  || ||||| ||    || ||          | |  || || |||  ||||  | |||||||  | || |  |||||||| || ||| |||| ||  | |||| |||||| ||||| |||||||| |||||||| || ||||||||||| || || ||
gtttactttcaat--ttcttttcgtttggacttactattattgttgctctaaatcttgggatcatatatatttgctttgtgtttttggttcagCTGATGCCTATACTCATACAGACTCTGAACTTCTCAAGTCAGAAAATAGTCATACTAGAGATGCTGGTTCAACTGCTTCCACAGCTATTCTCGTTGGTGA

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 4
----------gtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtg--gttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA
            |  |    | ||||     | ||    |||    || |  ||   ||  |||||   |   ||  | | || ||    || | | |||||||||  | ||||| || ||||| ||||||||||||||| | |||| || ||| | ||| |||||||| ||||||||||| || ||||| ||||| || ||
gtttgtttcctgactgtgccagtaatgt-cactttctatagcctgtatgaa-gtgttcactctaaatactactgtcttaaattatcc--tctgtacatgcagCTGATGCATACAAGCACACAGACTCAGAATTTCTGAAATCAGAAAATAATCAGAATAGAGATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGA

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|5003494|gb|AU068643.1|AU068643
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|5803440|gb|AI978410.1|AI978410
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CNGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29668036|gb|CB664311.1|CB664311
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29639786|gb|CB644795.1|CB644795
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|58670044|gb|CK058730.1|CK058730
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29666851|gb|CB663126.1|CB663126
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29688008|gb|CB684283.1|CB684283
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|33680351|gb|CF308590.1|CF308590
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29686520|gb|CB682795.1|CB682795
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCATAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|218495837|gb|FG960245.1|FG960245
EST:     AATTTAATTAATGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: AATTTAATTAA-GCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|44671917|gb|CR285351.1|CR285351
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29640127|gb|CB645136.1|CB645136
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA
              acctaaa  putative branch site (score: 3)
                                 tttctctgtacttttc  putative PPT
                                         tactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG