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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67126.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagt-tgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggat-tgttgatctgtattagtagctcatgtggatatacttctcttctt-ctgcag
|| |||||| ||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| || || || |||||||||||||||||||||||||| | |  |  | || |    ||  |  | |  | || |  |    |  |||||   | |  ||||||    |     | ||| |    |    | || |   | | || | | | || ||| |  | ||   | |||    |    |    |  || || | ||||
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTGTCTTTGGTGCCCTCAAGgtatat-atcttctgtttgttaccat--gatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgcttg-ctgtaagagtcatctcttgttgtggtgaacgat-ttcccatctctctagcccctttaacgtttgttgccgcag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgt---tgtgctttgatctca-actgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttt-tagaaacacaaccgtcaatataacctttg----gattgttgatctgtattagtagctcatgtggatatacttc--tcttcttctgcag
|| |||||| ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||||||||||||||||||   |   |    |||||| |||   ||||   |  ||   |  | |||  |   |  ||     ||   | | || |  | |||  |  |||        |||   | | |||     || || |  ||  | |  |||| |  |     | |  | |  | |  | ||||||
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTGTCTTTGGTGCCCTCAAGgtacatgtcttccttttgatgtcatgatgttatat-ttggggtgtttgtttgtagttagctcattaatagtaataataatttttttgcatgaacttgttgtacaaggcatcttttatggtgactggttttccatctctgtagttttttaacgtttgttgcattatgttgctgcag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
|| ||| || ||||| || || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||||||||||||||||||||| | ||     || |||   | || | |    | ||   ||  |  ||||    ||||    |    |  |   |   | | |  || ||     |  |||  | ||                                                        
CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattccttctttatcatgaatgattg----tatacatatgatacattttc--cttgtgttttggttgtaggtggcttatcaagaaaac--ttttttatacgatct--------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 |  || ||||| || ||    |||||||| |||||||| ||| | |||||||| ||  ||||||| || || ||||| || |||||||||||||| |||||    | |  |   |   ||||| ||||    | | ||  |  || | | ||   |  ||  | | | |  | |    ||  ||                                                                               
TTCAGTGGAACCTGCCGAGAGCAGGAGGCCATTCCGTGCACTCCTTGATGTTGGTCTTGTTAGGACTACAACAGGAAATCGCGTCTTTGGTGCCCTTAAGgtaatctctaat---actgcaactcttgg----tatgattttgttttagtggtgg-tcaaatctaataattgtgatggtttacag-------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G06590.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtg---tgttgtgctttgatctcaactgttg-gctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || || || |||||||| ||||||||||| |||||    | |  | || | || | ||    || | |  |||  |||| ||||||     | ||||| |    ||   | |    ||  ||                                                                               
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcatactgtaatgttaatcagtgtgattttgttttaatggttgat---caaattgaata----atctgtgattgtttacag-------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G06580.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtg---tgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || || || |||||||| ||||||||||| |||||    | |  |||| | || | ||    ||     | |  |||| ||||||     | ||||| |    ||   | |    ||  ||                                                                               
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcatgctgtaatgttaatcagtgtgattttttttaatggttgat---caaattgaata----atctgtgattgtttacag-------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || ||||| |||||||||||||||||||| |||||    | |  |   |   ||| || |   || ||| ||  |  || | | || |    |      ||||  | |    ||  ||                                                                               
TTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTGTCTTTGGTGCCCTTAAGgtaatctatcat---actgcaa-tgctaattggtgtgattttgttttaatggtgatcaaattgaataattttttattgtttacag-------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgt---gtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 | ||| |||||| |||||   || || ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||| |||||||| ||||||||   ||||| |  | || |      ||||     ||||  || ||||   ||  | | ||||| || |   | | ||   ||||    || ||  | ||   | |      || |    |                                              
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgta-tagtgtgttcatgatttgaagatgatgct-agcaatccttt----aatacc-ctgttggtttgcttcatgaaactatag--------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G25520.1 (Arabidopsis thaliana), 5'ss of exon 5
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag
 |  ||||| ||| |||||  |||||| ||||||||||||||  | |||||||| || || ||||| || || ||||||||||| || ||||| || ||||| |    |   ||| |      | ||   || ||| |      || |||||||| |    | ||     ||  |   ||| ||    || |  | | |||||  | ||||| | | || | || ||  ||||                               
TTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTGTGTTCGGTGCTCTTAAGgtat----taacttgtttctctttttt---tgttgtgagtgctctt-atttgtcatt----cttcttgagca--aatgcttatactggca-attctttaatatc-cttttggttcgctg-tttgaatctgtag-------------------------------

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|88766068|gb|CI775158.1|CI775158
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218499062|gb|FG952648.1|FG952648
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|58688294|gb|CK076981.1|CK076981
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|2443100|gb|C74871.1|C74871
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|33794896|gb|CF323328.1|CF323328
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|55410467|gb|CV722843.1|CV722843
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218483963|gb|FG953648.1|FG953648
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAAGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|88741629|gb|CI765137.1|CI765137
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218499324|gb|FG966003.1|FG966003
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|88736334|gb|CI759842.1|CI759842
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|396941604|gb|HO188261.1|HO188261
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|86898441|gb|CI292329.1|CI292329
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|4879230|gb|AU063529.1|AU063529
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218497228|gb|FG948508.1|FG948508
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|163927771|gb|EG712507.1|EG712507
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT

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: 75 (upstream exon), 75 (downstream exon)
Score: 448

CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT




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