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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G862219_T03 (Zea mays), 3'ss of exon 9
gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatag--agtaatccagtcctggt-accaacttttga-gtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG-----------------------
|||  |      ||   |  || || || | ||  | |  |  ||   |  |      || ||  |   ||| |  || | | |    |||  ||| ||||| || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||                       
gtaccggc----caacactcttccgattctgcttctgccgtgccaaactataagctcggtgatgtaaatctgcttgcctattctcactgtgtgcaagcagGTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGGTACGTGGCGCCATACGTTCTGA

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 9
gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatag--agtaatccagtcctggt-accaacttttga-gtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
|||  |      ||   |  || || || | ||  | |  |  ||   |  |      || ||  |   ||| |  || | | |    |||  ||| ||||| || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||
gtaccggc----caacactcttccgattctgcttctgccgtgccaaactataagctcggtgatgtaaatctgcttgcctattctcactgtgtgcaagcagGTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA03G07540.1 (Glycine max), 3'ss of exon 9
--gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaactt-ttgagtgccc---aaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
  | ||   |   |  |   || |  | || |  |    |||  ||||||  | |    ||   || | |   | |  | || || |   | |   |||||||| |||||| ||||||| || ||||| || |||||||| ||||||||||| |||||  | |  ||| | || ||  |
ttgcatcagttaattttttaatatgtgtttgtcatctgtcatgcacatgt--cttgatttacatcattaccattgcttatttgtttaacactcttaaaacagGTACTTGCTGTTTCACGCGTAATGGTTGCTTGGCAACCCATTGGTATATCGATGGGCATCTACGATATGTGTCACAG

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 9
------gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
        ||   ||| || |  |||| |   || | ||  ||     |  |||||| ||   |   ||| |  |  | | || |           |||||||| |||||| |||||||||||||||| || |||||||| || || || |||||||| |  | |||| | || ||  |
tgcctctgatgcttatctcctctcattgt-attttttcttgtatccatatctgttgcttaatttttcccattgtttat-ctaaataccaccattggaaacagGTGCTTGCTGTTTCACGTGTCATGGTTGCCTGGCAACCTATAGGCATTTCAATGGGAGCCTATGATATGTGTCACAG

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|29666427|gb|CB662702.1|CB662702
EST:     CTGAGGGAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GGTCCTTGCTATTTC
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagG-TCCTTGCTATTTC
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|14713699|gb|AU197670.1|AU197670
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|33683998|gb|CF312237.1|CF312237
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGCCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|13165132|gb|AU173929.1|AU173929
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|56157778|gb|C26441.2|C26441
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     AGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: AGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
 cattaac  putative branch site (score: 2)
                                  aactttt  TA-rich tract