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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatattttggatactgagctttttctggactgcaaacaattgaactattgaagatttcaggaagcattgtaatgaatatgtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 1
--ccatattttggatactgagctttttctggactgcaaacaattgaactattgaagatttcaggaagcattgtaatgaatat-gtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
     | ||||| | |  || |||| |||   |||| | |||||||||  |   | |||  |  |    || |||||| | | |  ||||||| |||||| ||||| |||||||||||||||||||||| || || || ||||| |||||||| |||||||| ||||||||||| ||||| || |||||||| || ||| |||
ccatgtgttttgaacatggacctttatctatgctgccagcaattgaac--tcacatattcaataagtttttttaatgatttttgaaaaaatgt-ctcatgtagGGTTTGAAAACTGCCATAATTGAGGGAGACGTCGTGGGTGGAACTTGTGTCAACAGAGGCTGTGTTCCGTCAAAGGCTCTCCTTGCTGTAAGTGGTAGGA

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 1
--------ccatattttggatactgagctttttctggactgcaaacaattgaactattgaagatttcag-gaagcattgtaatgaatatgtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
         |||||||| |    | |    |      | |||  |    |||| | ||  |   ||| | |||   ||| || ||  | |||            |||||||| ||||||| |||||  ||||||| || || || || ||||| |||||||||||||| |||||||| || ||||| ||| | ||||| || ||||| |
ggacaaaaacatatttttgcctttaactaatgaagaaattgcgtattgctgaagttttatattcttcggagaaattttgaaacgaggaagtgg---------tttgcagGGTTTGAAAACGGCCATTGTTGAGGGAGACGTGGTTGGAGGGACATGTGTGAACAGAGGATGTGTTCCTTCTAAGGCTCTTTTGGCTGTGAGTGGTCGAA

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 1
ccat-attttggatactgagctttttctggactg-caaacaattgaactattgaagatttcaggaagcattgtaatgaatatgtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
  || | |   || | |||   |  |     ||| |       | || ||       | |||        ||  ||   | |    ||  | |    |||||||| ||||||| |||||  | || || ||||| || || ||||| |||||||||||||| |||||||| || || || ||| | || || || ||||| |
--atgaatcaagaaattgatagtcgttgatgctgactgtgggataaagtaagttgagtatcacatttttgtgagataggttttattaacggcatgattgcagGGTTTGAAAACAGCCATTGTGGAAGGAGATGTGGTGGGAGGGACATGTGTGAACAGAGGCTGTGTTCCTTCCAAAGCTCTTTTAGCCGTGAGTGGTCGTA

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 1
ccatattttggatactgagctttttctggactgcaaacaattgaactattgaagattt-caggaagcattgtaatgaatatgtgaaaatgtactcatgc-agGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
            |    || || || |  |     |     ||||   |  ||||||| |       ||| |    || ||  |  | | |  |  ||  |||| || ||||| ||||| ||||| || |||||||| || ||||||||||| |||||||| ||||| || || || || ||||||||||| || ||||| |
-----------gtttgaagtttcttatataacctgatttgatgaaa-gtaaaagatttgctctgcttattatgg-aaacattggtgattttgtttgtgttagGGACTTAAAACAGCCATTATTGAAGGAGATGTTGTTGGAGGGACTTGTGTTAACAGAGGATGTGTGCCTTCTAAAGCTCTTCTTGCTGTTAGTGGTCGAA

upper sequence: LOC_Os01g23610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 1
ccatattttggatactgagctttttctggac-tgcaaacaattgaactattgaagat-ttcaggaagcattgtaatgaatatgtgaaaatgtactcat--gcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
    ||| |  | | | |  |  || ||    |||       ||     ||   ||| |||| |       |    |||||  |  |||  || | ||   |||||||||||||||||||| |||||||| ||||| || ||||| || ||||| ||||||||||||||||| || || || ||||| ||||| || ||||| |
----attgtaaaaagttaattagttgtgtgtgtgcgtgtgcgtgtgtgtttattgatattcaagtcattaagggtggaataattttaaaaataattattgacagGGTCTGAAAACTGCCATCATTGAGGGAGATGTGGTGGGTGGAACATGTGTAAACAGAGGTTGTGTTCCTTCTAAAGCTCTTCTGGCTGTAAGTGGTCGAA

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|58675783|gb|CK064470.1|CK064470
EST:     TTGGGGCGGGCGTCGGCGGGCACGGCGCAGCTCTCCACGCCGTCGAGAAG                         GGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTG
genomic: TTGGGGCGGGCGTCGGCGGGCACGGCGCAGCTCTCCACGCCGTCGAGAAGgtatgcttcg ... actcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTG
EST: gi|58670429|gb|CK059115.1|CK059115
EST:     TTGGGGCGGGCGTCGGCGGGCACGGCGCAGCTCTCCACGCCGTCGAGAAG                         GGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTG
genomic: TTGGGGCGGGCGTCGGCGGGCACGGCGCAGCTCTCCACGCCGTCGAGAAGgtatgcttcg ... actcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgaagatttcaggaagcattgtaatgaatatgtgaaaatgtactcatgcagGGTCTGAAAACTGCCATAATTGAGGGGGATGTTGTAGGTGGGACTTGTGTGAACAGAGGTTGTGTTCCGTCGAAGGCACTTCTTGCTGTCAGCGGTCGGA
                     attgtaatgaatat  TA-rich tract