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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAGGCTCCTTTCGTGACCAAGGCTGAGAAGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccctctccacaactctgcacctgcaactgtcatgacacattgaaactgatctgttgtgcgtttctcgttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g37910.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g37910.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G066528_T02 (Zea mays), 5'ss of exon 6
GACAAGGCTCCTTTCGTGACCAAGGCTGAGAAGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgta-atccccctctccacaactctg--cacctgcaactgtcatgaca-----cattgaaactgatctgttgtg-cgtttctcgttgcag
|| |||||||| | |||| | ||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||| |      |   | |||||||      | |    ||    || |     | |||       |    |||| | | |||||||||||
GAGAAGGCTCCCTACGTGTCTAAGGCAGAGAAGCTCAAGGCTGAGTACACCAAGAAGATCGACGCTTACAACAACAAGCAGgtacagtatgttacactcaactctcgttgtccggcgttgcttcgaaattcctctttgcggtgcgtgacatgtgtcatctctcgttgcag

upper sequence: LOC_Os09g37910.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G162284_T02 (Zea mays), 5'ss of exon 6
GACAAGGCTCCTTTCGTGACCAAGGCTGAGAAGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgta-atccccctctcca-caactctgcacctgcaact-gtcatgacacattgaaactgatctgt----tgtgcgtttctcgttgcag----------
|| |||||||| | |||  | ||||| |||||||| |||| ||||||||| |||||||| |||||||| ||||||||||||||  |      ||| || | ||||  | |  |   |  | |||  | |   | || |  |||||    |||| ||  |  || |             
GAGAAGGCTCCCTACGTATCTAAGGCCGAGAAGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatgttctacatctactccactcacgttgcccggcattgc-ctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcag
















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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAAGGCTCCTTTCGTGACCAAGGCTGAGAAGCTCAAGGCTGAGTACACCAAGAAGATTGACGCCTACAACAACAAGCAGgtaatccccctctccacaactctgcacctgcaactgtcatgacacattgaaactgatctgttgtgcgtttctcgttgcag

- - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG