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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attattgatgtttaagatgacctggaatctgatctttacacttactgtaattcatgtcctggtaatatgttgtgcatgatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 8
attattgatgtttaagatgacctggaatctgatctttaca---cttactgtaattcatgtcctggtaatatgttgtgcatgatgtaatt-tgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
  | |  || |   ||      |    | | ||  |||||   |||| ||  |||| ||   ||    ||||   | | |||| |  |    || ||||||||||||| |||||||||||||||||||| ||| | ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||
--tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgc--gtatgcacttcctgatttgctcacattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
attattgatgtttaagatgacctggaatctgatctttacacttactgtaattcatgtcctggtaatat--gttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
     || |  |   |  || | || |||  |  || |  |||  |  |  |  | |  | |||   |  |||| || | ||    || | ||  |||| ||||||| || ||||  || || || ||||| || |||||||||||| |||| |||||||||||||||||||| || || ||  ||||  |||| || |||||
---gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
attattgat-gtttaagatgacctggaatctgatctttacacttactgtaattcatgtcc-tg-gtaatat--gttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
    | |||    ||  || |  || || ||  |||||| | ||| | |  ||  | |   || |||   |  |||| || | ||    || | ||  |||| ||||||| || ||||  || || || ||||| || |||||||||||| |||| |||||||| ||||||||||| || || ||  ||||  |||| || |||||
---gtggatcaggtatcataaattg-aacct--tctttaaaattatttttctttttttttgtgtgtagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 7
attattgatgtttaagatgacctggaatctgatct-ttacacttactgtaattcatgtcctggtaatatgttgtg-catgatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
   | ||| |   |  || | |||    ||  | | ||   |  |||    | ||| |       ||  ||||   | |||    |  | ||  |||| ||||||| || ||||  || || || ||||| || |||||||||||| |||| |||||||||||||||||||| ||||| ||  ||||  |||| ||||||||
-aaagtgaagga-agaataatctgcttccttttttgttttgcccactcagttccattttaaaagtattggttgaatcttgaccctaaatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATCCGTCTTGTTGACTTGCGGCAATCAGC

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
-attattgatgtttaagatgacctggaatctgatctttacacttactgtaattcatgtcctggtaatatgttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
    | ||| |   |  || |  ||   ||| || |||   | | ||    | ||| |       ||  |||| || | ||    |  | ||  |||| ||||||| || ||||  || || || ||||| || |||||||||||  |||| |||||||||||||||||||| || || ||  ||||  |||||||||||||
gcaaagtgaagga-agaataatttgctttct-atttttttgcctgctcagttccattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC

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|58675521|gb|CK064208.1|CK064208
EST:     GAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     GAGCTTC-ATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCACTTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCA-TTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
EST: gi|2310581|gb|C26736.1|C26736
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     GAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAGCTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58588909|gb|CF987217.1|CF987217
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACAT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACAT
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|33796287|gb|CF324010.1|CF324010
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTNGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGT-GCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     GAAGCCTCCAAACATGGAAGA-CTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAGCTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattcatgtcctggtaatatgttgtgcatgatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
                                         tgttgat  putative branch site (score: 4)
                                    taatttgttgatattt  TA-rich tract