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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