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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactggtttacgcatgctcatgccacatgatgcttctagaattattcagactaacatgtatcttgtattcctgtgtggtttgtgtttggtctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTCAAAATAAAATGCTAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g17930.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G107731_T02 (Zea mays), 3'ss of exon 5
--atactggtttacgcatgctcatgc-cacatgatgcttctag--aattattcagactaacatgtatcttgtattcctgtgtggtttgtgtttggtctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTCAAAATAAAATGCTAAAG
    ||||||  | ||| | || ||| |  |  || | ||||   |    || | | | | || ||  |   |||    |||  ||| | |||||   |||||||| |||||||| ||||| | |||||| |||||||||||||| |||||||||||||| ||||||||||||
atgaactggtgcatgcacg-tcgtgctcgtagaattcatctaattagcatttgacatttatatctacttaacatt----tgtcatttatatttgggtccttgcagCCATTGCAGTCAAAGATAGACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG

upper sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015730_T03 (Zea mays), 3'ss of exon 5
----------atactggtttacgcat------gctcatgccacatgat--gcttctagaattattcagactaacatgtatct-tgtattcctgtgtggtttgtgtttggtctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTCAAAATAAAATGCTAAAG
          |||||   | || | |      |   ||  |  | |||  | || |     |||  |  | |   |   |||   ||  | | |||  ||| |||||||   |||||||| |||| ||||||||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||
gtagatttctatactatctcacccttttgatggtatatatctgaagattggttttttatggtatgaatccaattttccctctacttaaacgtttgtcatttatgtttgggtccttgcagCCATTGGAGTTAAAGAAAAACTAGAATCTCTTTGTAGGGAGTTTCAGCGTCAAAACAAAATGCTAAAG

upper sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015730_T04 (Zea mays), 3'ss of exon 3
-atactggtttacgcatgctcatgccacatgatgcttc-tagaattattcagactaacatgtatcttgtattcctgtgtggtttgtgtttggtctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTCAAAATAAAATGCTAAAG
 |  ||  |    | ||     ||     || |  ||  | | || | ||  | |  |      |||  |  | | |||  ||| |||||||   |||||||| |||| ||||||||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||
cacccttttgatggtatatatctgaagattggttttttatggtatgaatccaattttccctctacttaaa--cgtttgtcatttatgtttgggtccttgcagCCATTGGAGTTAAAGAAAAACTAGAATCTCTTTGTAGGGAGTTTCAGCGTCAAAACAAAATGCTAAAG

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|33809156|gb|CF330462.1|CF330462
EST:     GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAG                         CTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC
genomic: GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAGgcaagcttct ... tctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC
EST: gi|29639433|gb|CB644442.1|CB644442
EST:     GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAG                         CTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC
genomic: GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAGgcaagcttct ... tctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC
EST: gi|40490411|gb|BX899913.1|BX899913
EST:     GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAG                         CTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC
genomic: GTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAGAGAGGGATGCAGgcaagcttct ... tctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagactaacatgtatcttgtattcctgtgtggtttgtgtttggtctcttgcagCTATTGCAGTTAAAGAGAAACTAGAGTCTCTTTGTAGGGAGTTTCAGCGTCAAAATAAAATGCTAAAG
    gactaac  putative branch site (score: 1)
                                             tctcttgc  putative PPT
                  ttgtatt  TA-rich tract