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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttgactgcatctggttctattataatacgcatttatacgcttcaatttcttatttgattctgcttcatgtttttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG

Basic information

species Oryza sativa
transcript LOC_Os10g27230.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 3
gtatatttgactgcatctggttctattataatacgcatttatacgcttcaatttcttatttgattctgcttcat-gtttttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
|||  ||||| |   | |   | | |||  ||  |  ||  |||  || | | || | |||||| ||||| | | | | | | |||| ||| |||||  ||||   ||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||| |||
gtaactttgagtttcttttactttgtta--atttgatttggtaccttttactgtcctgtttgatactgctcctttgctgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGCTGTGCTACTTTTTTCCGCAGAGACAAGTTTTCGCATGTTAAAAAATACGAG

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 3
gtatatttgactgcatctggttctattataatacgcattt-atacgcttcaa---tttcttatttgattctgc--ttcatgtt---tttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
     | | || | ||   | | ||||||| |     | | |||   || ||   ||  || |||  ||  ||  || ||| |   || | ||||||| | ||||     | || | || ||||| ||||| || |||||||||||||||| ||||||||| || ||||||||||||
---gttgttacagtattcagatttattatagttttagtctcataatttttaaatgttattttttttgttaagcggtttatggtgggttcacagGTATACAATGGAAACATTAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTGAAAAAATATGAG

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 3
gtatatttgactgcatctggttct-attataatacgcatttata-cgcttcaatttcttatttgattctgcttcatgtttttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
|| | ||  | |   |||||| ||  | || |||  | |||| |    || |  | || |  || || |     |||  |||| |||| || | |||     |  || | || ||||| ||||| || |||||||||||||||| ||||||||| ||||| ||||| |||
gt-tgttgcaatat-tctggtccttgtgatcataaacttttaaagtattttagatgctaacctgtttat----tatgggtttacagGTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAG

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G39210.2 (Glycine max), 3'ss of exon 3
gtatatttgactgcatctggttctattataatac-gcatttatacgcttcaatttcttatttgattct-----gcttcatgtt--tttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
     | | ||   ||   | | ||||||  |     | || ||   || || ||  | ||| || ||     | || | ||   || | |||| || | ||||     | || | || ||||| ||||| || |||||||||||||||| |||||| || || ||||||||||||
---gttgttacgttattcagatttattatggttttagacttgtaatttttaaatttcttttttatgctaagctgtttaaggtgggttcacagGTTTACAATGGAAACATTAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCTCATGTGAAAAAATATGAG

upper sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G26620.1 (Glycine max), 3'ss of exon 3
gtatatttgactgcatctggttct-attataatacgcatttatacgcttcaatttcttatttgattctgcttcatgtttttaa-agGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
|| | ||  | |   |||||||||  | || |||  | || | |   ||| |  |  ||     || |  |    ||||  || |||| || | |||     |  || | || ||||| ||||| || |||||||||||||||| ||||||||| ||||| |||||||||
gt-tgttgcaatat-tctggttcttgtgatcataaactttaaaaatattctagatggtaacctgtt-tattgtgggtttacaacagGTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATATGAG

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: 71 (upstream exon), 75 (downstream exon)
Score: 25

GTGCAACTGAACCACTTCGAAGATTTTTTTTCACCCGAGCTTGATAAACATGGATATCAGGCACTTTACAAGAAAAGGACAACAGAGgtatatttga ... gtttttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacgcatttatacgcttcaatttcttatttgattctgcttcatgtttttaaagGTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAG
                            atttgat  putative branch site (score: 25)
                                            tgttttt  putative PPT
                    aatttcttatttgatt  TA-rich tract