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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g31840.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 4
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttat-tctgttgagtaatatgtgttctcttttgcataat-catgatgcag
 ||||| ||||| ||||| || |||||||||||||||||||| ||||||||  || | |||||||| ||||| ||||| |||||||||||||| |||||||||||| || |    | ||||   ||||   | ||| |   || ||| | || ||||||    | |  ||| || ||| |||  |||||
TCATATATTCTTTCAACAAAGGCATGGTCCAGGCCAAAGATCATTGTATAACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattc--tattgtttacacaattcattttgcag

upper sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 5'ss of exon 3
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcag
|||| | |||||||||||||||||||| || || ||  | ||| | || |||||||||||||| |||||||| | ||| || ||||| || || || |||||||   | |  |   |  |  |  |||  |   |      |   | ||   |||||| || ||  |||   |  |           
ACATGTATTCTTCCAACAGAGACATGGACCTGGGCAGCGGTCCCTCTACAATGTTCTAAAAGCTTACTCTGTCTTTGACAGAGATGTAGGCTATGTTCAGgttttactcagga--acccatcacctttctgtgcttgttacaaagtatttcataatat-tgatcattttaaaactacag--------

upper sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 5'ss of exon 4
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcag
|||| ||||||| ||  |||||||||| || || |||||||||||||| ||||| || || |||||||| |||||||| || ||||| ||||| || ||||| | |  |  |  |  |  |    |||   || |    || || |  |  |  |      |||    ||  |  |||    |||||
ACATGTTTTCTTTCAGAAGAGACATGGACCTGGGCAAAGATCCTTGTACAATGTCCTTAAGGCATACTCAGTTTATGACAGAGATGTCGGATATGTTCAGgtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatc----tgcag

upper sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 5'ss of exon 4
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgca-taatcatgatgcag
|||| ||||||||||  |||||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| || ||||| ||||| || ||||| | |    | |    |  ||   ||     |||   |  |   || |    | || |         | | | |||  || ||||||
ACATGTTTTCTTCCAGAAGAGACATGGACCAGGCCAAAGATCATTATACAATGTTCTAAAAGCATACTCTGTCTATGACAGAGATGTCGGATATGTTCAGgtatttccagagatcttttcctttattc---ttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcag

upper sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 4
ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgttaaaactg-ctgactagttttaggatataaacttattc--tgttgagtaatatgtgttctcttttgcataatcatgatgcag
|||| |||||||||| ||||||||||| || || ||||| ||| | || |||||| | || ||||||||||| ||||| || ||||||||||| || ||||||||  |   |  |  || |  | | ||    |      || |    |  ||| | | ||  | |   | | |  | |     ||||||
ACATGTTTTCTTCCAGCAGAGACATGGACCTGGTCAAAGGTCCCTCTACAATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttga----aatgcag

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|29666046|gb|CB662321.1|CB662321
EST:     ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAG                         GGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
EST: gi|218502114|gb|FG959502.1|FG959502
EST:     ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAG                         GGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
EST: gi|29666045|gb|CB662320.1|CB662320
EST:     ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAG                         GGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT