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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtccttcccctgtctttgcatgggaattctgagatattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC

Basic information

species Oryza sativa
transcript LOC_Os03g50620.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 5
---atgtccttcccct-gtctttgcatgg--gaattctgagatattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC
   ||||| |||   | ||  ||  ||    |||  || | ||||||      | || || | |  |  | |  |   ||| ||   |  ||| ||| || |  ||||||||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| ||||||||||||||||| ||||| ||||||||||||||
agtatgtctttctaatagttattatatacatgaaaact-acatatttacag--ggttgacattatgtgtagtggt--taataagcttctgcatgttgcttttt-agGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 7
---atgtccttcccctg-----tctttgcatgggaattctgagatattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC
   ||||| |||   |      | | | ||||  || |   | ||||||      | || || | |  |  | |  |   ||| ||   |  ||| ||| || |  ||||||||||||||||||||| ||||| ||||||||||| |||||||| || ||  |||||||||||| |||||||||||| ||||| ||||||||||||||
agtatgtctttctaataattattatatacatgaaaact---acatatttacag--ggttgacattatgtgtagtggt--taataagcttctgcatgttgcttttt-agGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGGAAAATTTTCAACGTTTGCGCTGTTTACCTTCTTGATTC

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G39880.1 (Glycine max), 3'ss of exon 5
atgtccttcccctgtctttgcatgggaattctgaga-tattttagattgtttaacttcacctaaaatcatgac-aatgag--agaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC
 || |  |  |  |  | |  | |   ||  | | | ||   |    || || || | ||   | ||| |||| ||| |   |  |    || ||||| | |||| ||||| ||||| |   | ||||||||||| ||    || ||||| ||||||||||||||||||||||| |  ||||||||||| ||| | ||||||||
ttgccagtttctagaatgttgaagattatcttaaaaataaagttttatggttgacctgac---agatcgtgaccaatcaactatgctttgtaatgttt-tgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 3'ss of exon 4
atgtccttcccctgtc--tttgcatgggaattctgagatattt-tagattgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC
 || |||| |||  |   | ||||       |      | ||| |   || ||| |  |    | |  | || |        | |  || ||| ||| |  ||||||||| || || ||  | ||||| ||| | || || || ||||| || |||||||| || || |||||||| ||||||||||||||||| ||||||||
-tgcccttgcccaatagatatgcacccagtatgcatattgtttgttttttttttcagctggattgatcttataaattctttggtcttcacattctttat--agGCCAGATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTC

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|86530562|gb|CI170768.1|CI170768
EST:     ATGATGACTATCTTGTGTTTGATTGCACAG                         GCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC
genomic: ATGATGACTATCTTGTGTTTGATTGCCCAGgtaactttct ... gtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC
EST: gi|58611474|gb|CK039186.1|CK039186
EST:     GCAACTGGAGGGTTATTTGGATGATGACTATCTTGTGTTTGATTGTCCAG                         GCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC
genomic: GCAACTGGAGGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAGgtaactttct ... gtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC
EST: gi|426369|gb|D22232.1|D22232
EST:     GCAACTGGAGGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG                         GCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC
genomic: GCAACTGGAGGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAGgtaactttct ... gtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC
            acctaaa  putative branch site (score: 3)
                                           ttgtttctcc  putative PPT
               taaaatcat  TA-rich tract