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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtagatgctcatgcatgtggactaggttgtattcatatctaatttagaaggcgtttgcaccacgcaatatttctatactgatgatccttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGGTCATGGAATGTGATAATGTTTTTAACACTGGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g74640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 7
-gctgtagatgctcatgcatgtggactaggttgtattcatatctaatttagaaggcgtttgcaccacgcaatatttctatactgatgatccttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGGTCATGGAATGTGATAATGTTTTTAACACTGGAGCAG
   ||||| | |  | |||  |  | |||| | ||| |||   | | || |    | | | ||  | |  ||   ||   || |||| |  |||||| ||||||| |  |||||| || || || ||||||||||||||||| || |||||||||||||||||||||||||||||||| |||||||||
tcatgtaggtccaaaagcaaatctattaggatttat-catgcttgagtttggcaacatgtacatgaagtgatgagtcgtaaccgatggttattttctacagGGACCTTGTGCTTTCTACAAGGGATTCATTGCAAACTTTTGTCGGATTGGGTCATGGAATGTGATAATGTTTTTAACTCTGGAGCAG

upper sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 8
----gctgtagatgctcatgcatgtggactaggttgtattcatatctaatttagaaggcgtttgcaccacgcaatatttctatactgatgatccttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGGTCATGGAATGTGATAATGTTTTTAACACTGGAGCAG
      ||  |  |     |   |  |    ||  ||  |   || |  |||  |      |  ||| |  ||    |     ||  | | |  |||||| ||||||| |  |||||| || || || ||||||||||||||||| || |||||||||||||||||||||||||| ||||| ||||| |||
gctaattggggggggggggggggggagggggggacgtggtgtcatgtgttttgcagaaaactgtcactaatcaggcata----acctacggttattttctacagGGACCTGGTGCTTTCTACAAGGGATTCATTGCAAACTTTTGTCGGATTGGGTCATGGAATGTGATAATGTTCTTAACTCTGGAACAG
















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|29663991|gb|CB660266.1|CB660266
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
EST: gi|29682716|gb|CB678991.1|CB678991
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
EST: gi|87026198|gb|CI278322.1|CI278322
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
EST: gi|88474187|gb|CI411458.1|CI411458
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
EST: gi|88509850|gb|CI437356.1|CI437356
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
EST: gi|33684429|gb|CF312668.1|CF312668
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAA-GGGTTCATTGCAAACTTTTGCCGCATT
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATT
EST: gi|86890131|gb|CI321308.1|CI321308
EST:     CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGAT                         GGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG
genomic: CAACGTACAAGAGTACACTAGACTGTTTTGCAAAGACATTAAAGAATGATgtacggcaaa ... ttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaaggcgtttgcaccacgcaatatttctatactgatgatccttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGGTCATGGAATGTGATAATGTTTTTAACACTGGAGCAG
                                 tactgat  putative branch site (score: 2)
                                          tccttttctgc  putative PPT
                       aatatttctatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtagatgctcatgcatgtggactaggttgtattcatatctaatttagaaggcgtttgcaccacgcaatatttctatactgatgatccttttctgcagGGACTTCCTGCTTTTTATAAAGGGTTCATTGCAAACTTTTGCCGCATTGGGTCATGGAATGTGATAATGTTTTTAACACTGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG