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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_Os08g31840.2
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|29666045|gb|CB662320.1|CB662320
EST:     ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAG                         GGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
EST: gi|218502114|gb|FG959502.1|FG959502
EST:     ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAG                         GGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 22 (upstream exon), 69 (downstream exon)
Score: 6

ACATATTTTCTTCCAACAGAGACATGGTCCAGGCCAAAGATCCTTGTATAATGTTCTAAAAGCATACTCTGTTTATGATAGGGATGTTGGATACGTGCAGgtttgtgtta ... catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA




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