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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggatggataaattcaaatgttttgccaatttgaattgttgaactattgtggtgctattgaagcaatgtagcatggaataatttgtaaatatgctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT

Basic information

species Oryza sativa
transcript LOC_Os06g34690.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069765_T01 (Zea mays), 3'ss of exon 9
gtaagggatgg--ataaattcaaatg-ttttgccaatttgaattgt-tgaactattgtggtgctattgaagcaatgtagcatggaataatttgtaa-atatgctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT
||||| |||    ||  |    |||| |||| || |  |  | ||  || |  ||| |   |  |||   | |   |   | || ||| | |||   | |   |||| ||||||||||||| ||||||||||||||||||||||||||||||| || |  || ||| ||||||||||||||||||||||  | || |||||||| ||||||
gtaagagatatccatgtaccacaatgattttacctaaatacaatgcatgcataattttaaagtaatttg-gtagaattctaaggtatattatgtggcaaactttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCAAATTCTAAAATTCAAGCCTGATTTAGTCATAACTGAGAAAGGGCTCAGT

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 9
gtaagggatggataaattcaaatgttttgccaatttgaattgttgaactattgtggtgctattgaagcaatgtagcatggaataatttgtaaatatgctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT
||||| ||||   |  | | |   |  |     | || ||   |  | | ||   ||  | | | || | ||||   |  | ||  | || ||  |  |||| |||||||||||| |||||||||||||||||||| ||||||||||| || || || ||| ||||||||||||||||||||||| ||||||||||||| ||||||
gtaagagatgtccatgtaccacaatgatcttgctgtgcatgcat--agttttagagtaatttggtagaattgtaaggtatattatgtggtgaactt--tattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT
















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|58675550|gb|CK064237.1|CK064237
EST:     AGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
genomic: AGGAAGAAGATTGgtaagggatg ... gctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
EST: gi|218489854|gb|FG947528.1|FG947528
EST:     AAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
genomic: AAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGgtaagggatg ... gctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
EST: gi|163920886|gb|EG710373.1|EG710373
EST:     AGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
genomic: AGGAAGAAGATTGgtaagggatg ... gctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
EST: gi|58690265|gb|CK078952.1|CK078952
EST:     AAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA
genomic: AAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGgtaagggatg ... gctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCA

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: 73 (upstream exon), 60 (downstream exon)
Score: 24

GGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGCCCTGTTGAGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGgtaagggatg ... gctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtgctattgaagcaatgtagcatggaataatttgtaaatatgctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT
                                              ctatttc  CT-rich tract
                             aataatttgtaaatat  TA-rich tract