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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctgtttcttcgtatcattgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA

Basic information

species Oryza sativa
transcript LOC_Os05g39850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 6
gtcagtgctgtttcttcgtatcattgcttc-tgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
|| |||| ||||||     ||   || | | || | ||| |     |   | |||      |  ||  || |   |  | ||| || |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||| 
gtaagtgatgtttcagatcattgctgatacatgatttaattaataatgctttatttattcatccattcatttctatattttggcatacagAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCCCCTTTGGCTATCTCAACAACTGGC

upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 6
gtcagtgctgtttcttcgtatcattgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttact-tatgt-ggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
|| |||| ||||||     |||||| |       |  || || |||   |||||||  | ||  ||| | || || ||| | ||    |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| ||||| 
gtaagtgatgtttc---agatcattaca------gatacatgattttgttgattgtgttttatttatttatttctatattttggctctcagAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGC

upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------gtcagtgctgtttc---ttcgtatcattgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgc------agAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
                                                           |   || |   |    || |||| ||||        ||   | |  | |  |  |  || | |||   | |  |  |    ||   |||      || || || |||||||||||||| || ||||| || ||||||||||| || ||| | |||||  ||||||||||||| || ||||| || ||||| || || 
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC

upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------gtcagtgctgtt--tcttcgtatcattgcttctgttgtaacttgctttcaat----gattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
                                                            |||   | || |  | ||   |||   | |  | |  |   || || | |||    ||||||| ||  | | | |||| ||| | | ||       || || |||||||||||||| || ||||| || ||||||||||| || ||| | |||||  ||||||||||||| || ||||| || |||||||| || 
gttagagttttctcttgatctcctttctgttagttttttttgtcagctccttttctgttagtcgaagttggtattattgaaatccaagttggtctgctccttttctcttaatataagattgtaatgctagtctgtcttgcttctttagT-------GACATCAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACTACAGGC

upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------gtcagtgctgtttc----ttcgtatcattg----cttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
            | |   | | ||     ||||  ||||||    ||| |  | |||||   |||   |  ||    || ||| | |||||         |  | |||||| || |||||||||||||| || ||||| || |||||||| || || || || |||||| | ||||| ||||| ||||||||||| ||||| || || 
gtaagtcttgcttgaaaacagatttcagattcgactcattggatactttttgtctaactcatttttctttcttcacttgaaaacaaatcttgt-------gctttcagAGACATCAACATGATGATGGTTGGTGATCCATCTGTTGCCAAATCTCAACTTCTGAGAGCGATAATGAATATTGCACCTTTGGCTATATCAACCACAGGC

upper sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtcagtgctgtttct--tcgtatc--attgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
               || || ||     || ||||  |  ||| ||||  |||  |      |||  ||  |   |||  | | |  | |  |||    |  || || ||||||||||||||||| || |||||||| ||||||||||| || ||  |||||||  ||||||| ||||| ||||||||||| || || ||||| 
tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaat----caaatttttacatcttaataaaaccgaattcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT

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: 55 (upstream exon), 50 (downstream exon)
Score: 12

CTCCATCTATATATGGCCATCTGTGGATAAAGAAAGCAGTAGTTCTATTAATGCTTGGTGGTGTAGAGAAGAATCTGAAGAATGGAACTCACTTGAGAGGgtcagtgctg ... tggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgcagAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
                          taaatatatcttactt  TA-rich tract