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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgcatcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA

Basic information

species Oryza sativa
transcript LOC_Os03g02150.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 18
gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgcatcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
                                                                                              | | ||  |||   ||      |     | | |   | | | |  |||  ||||||| | || |||||  |   |||||| ||| || | ||| | ||||| ||||||| |||||||||||||||||||| |||||  |||||||||||||||||||||| |||||  |||| ||||||||||||||||| |||||| ||||  
----------------------------------------------------------------------------------------------gtaactc-cattgatag----gacactttctcttggtcaacgtcaatttattccattgagaaggattt--tccccttactgtgggtt-atttgccaaatct-agTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG

upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G092741_T01 (Zea mays), 3'ss of exon 3
gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgcatcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
                                                                                                       |  |  | |   |   ||| || | |  | |  |  |||  | | ||| | ||  |||  |    |||||| ||| || | ||| | ||||  ||||||| ||  |||||||||||||||| |||||| ||||||||||||||||||||||||||||  |||| |||||||||||||| || |||||| ||||  
-----------------------------------------------------------------------------------------------------gtaactccattgctaggatacaattttatct-tggtcaatttatgctattgagaagaattcctcccccttactgtgggtt-atttgccaaatcc-agTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG

upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 17
gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgc-----atcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
                      || |  | |  |  |      | | || | ||   |      |||  | |||   ||| |  |   ||||||       ||  | | ||  | |||||   |      | |  |||| | | ||        || ||| | | |  | | || |            ||| || ||   |||||  |  || | || || || ||||||||||| |||||||| ||||||||||||||||| || || ||    ||||| || || || | |||| | ||  
----------------------gtgtgtttatgggct------tcatatttgctcagaataggttattctatcattattttgaattccaaatctattagagattgtgcttggttgctctc---tggaggaaaattttatgtagtatgtaaattgttgacactaactgttatatcct------------cttttctaaatgtagTCCTCATTGCTTAAAAAAGCCGAAGATGCTGAAGTTGACACTGCAGAGCAAAGTGCTATCAAGTTGCGGGCACAGCAGCAGACTTCAAATGCTTTGGTTG

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: 72 (upstream exon), 75 (downstream exon)
Score: 26

TGAAATACAGCAGAGAGCAGTCGAATATTTTGAACTAAGCAGGAAAGGTGCTGCTTTGGCAGACGTGTTAGCAGAAATGCCGAAATTTCCTGAACGTGAGgtaaattttc ... cgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
                       ttcttac  putative branch site (score: 26)
     attaacaatgattt  TA-rich tract