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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccccctctccacaactctgcacctgcaactgtcatgacacattgaaactgatctgttgtgcgtttctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC

Basic information

species Oryza sativa
transcript LOC_Os09g37910.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g37910.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G066528_T01 (Zea mays), 3'ss of exon 6
----gtaatccccctctccacaactctgcacctgcaactgtcatgacacattgaaactgatctgttgtg-cgtttctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC
    || |  | |  |||      || |    |||    |  ||  | | |||       |    |||| | | ||||||||||| | |||| |||  |  | || || || || |||||||||||||||||||||||||||||||||||||                                 
gtatgttacactcaactctcgttgtccggcgttgct-tcgaaattcctctttgcggtgcgtgacatgtgtcatctctcgttgcagTCTGGAGACCCCACGGCGTCTGGTGATTCCGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGAG-------------------------------

upper sequence: LOC_Os09g37910.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G066528_T02 (Zea mays), 3'ss of exon 6
---------gtaatccccctctccacaactctgcacctgcaactgtcatgacacattgaaactgatctgttgtg-cgtttctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC
         || |  | |  |||      || |    |||    |  ||  | | |||       |    |||| | | ||||||||||| | |||| |||  |  | || || || || |||||||||||||||||||||||||||||||||||||                                 
gtacagtatgttacactcaactctcgttgtccggcgttgct-tcgaaattcctctttgcggtgcgtgacatgtgtcatctctcgttgcagTCTGGAGACCCCACGGCGTCTGGTGATTCCGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGAG-------------------------------

upper sequence: LOC_Os09g37910.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G162284_T02 (Zea mays), 3'ss of exon 6
-------gtaatccccctctccacaactctg--cacctgcaactgtcatgacacattgaaactgatctgt------tgtg-cgtttctcgttgcagGC---AGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC
        |  ||  | ||| | | ||||      || |  | || |  |  |  | |    ||   |||       ||| ||| | ||  ||||| |   |||||| ||  |    || || || ||||||||||||||||||||||| ||||||| ||||||||                                 
gtgcagtatgttctacatctactccactcacgttgcccggcattgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG-------------------------------

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|701299|gb|D47590.1|D47590
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTNACGGCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCG-CTNTTACAAGTCCAAGTCCGA
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGA
EST: gi|55414429|gb|CV726805.1|CV726805
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|33663560|gb|CF294527.1|CF294527
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|55435413|gb|CV730838.1|CV730838
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|86829652|gb|CI286813.1|CI286813
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|88728459|gb|CI751969.1|CI751969
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCCCGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|33664035|gb|CF295002.1|CF295002
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|572169|gb|D41680.1|D41680
EST:     AGTTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGAAG                         GCAAGGAGGCCCGGNTACCTTCAGGCG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCA-GGAGGCCCGGCTACCT-CAGGCG
EST: gi|701542|gb|D47833.1|D47833
EST:     AGCTCAAGGCTGAGTACANCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCCGGNTACCTCAGGCGACT
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCC-GGCTACCTCAGGCGACT
EST: gi|33691038|gb|CF319277.1|CF319277
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|33655319|gb|CF277933.1|CF277933
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|15008575|gb|AU222963.1|AU222963
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|55438827|gb|CV732712.1|CV732712
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|88576662|gb|CI670807.1|CI670807
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCC
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCC
EST: gi|33683487|gb|CF311726.1|CF311726
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|24208407|gb|AU225434.1|AU225434
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
EST: gi|88571600|gb|CI662973.1|CI662973
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCT
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCT
EST: gi|569750|gb|D40599.1|D40599
EST:     AGCTCAAGGNTGAGTACACCAAGAAGATTGACGC-TACAACAACAAGCAG                         GCAG-AGGCC-GGCTACCTCAG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAG
EST: gi|33823174|gb|CF337387.1|CF337387
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCCGAGGT
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCC-GAGGT
EST: gi|55437048|gb|CV731721.1|CV731721
EST:     AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACCACAACAAGCAG                         GCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG
genomic: AGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccc ... ctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgcaactgtcatgacacattgaaactgatctgttgtgcgtttctcgttgcagGCAGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC
                         aactgat  putative branch site (score: 3)
                                          tttctcgtt  putative PPT
                    attgaaa  TA-rich tract