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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggctatgcacaataagactcactacattcttttttctactcctttcccaggtatttgacagcttatgtttcttggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG

Basic information

species Oryza sativa
transcript LOC_Os05g01060.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 4
gtggctatgcacaataagactcactacattcttttttctactcctttcccaggtatttgacagcttatgtttcttggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG
||| |||  ||| |  |  ||   | |  |  | ||  | || |  ||    || ||| ||  | | ||| | ||   |||| || |||||||| || |||||||||||  ||||||||||||||||||| ||||| |||
gtgactacacactaacaatctttttcctgtaatgttctttcttcaatctgtagtgtttcact-cgtgtgtattttaacagGAGGCCCAAATACTTAATGAGAAACATGTCCTGGAAAAACGCATTGCATATATGCGCATG

upper sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G35770.3 (Glycine max), 3'ss of exon 7
------gtggctatgcacaataagactcactacattcttttttctactcctttcccaggtatttgacagcttatgtttct-tggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG
      |  |  |   |   | |  ||   || | | | |||| | |||  |  |||  |   |||| | | || ||||  |   |||||| ||||||||  ||||| ||| |||| |||||||| ||||||||||| |||||  ||
gtaaaaggtgtaaaatagttttaagctgtttagagtatattttgt-ctcaatgtccattttggtgactgatcatttttccataccagGAAGGACAAATACGGAACGAAAAATATGTCTTGGAAAAGCGCATTGCATATATGCGTCTG

upper sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 6
--------------------------gtggctatgcacaataagactc-actacattcttttttctactcctttcccaggtatttgacagcttatgtttcttggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG
                             ||| ||  | |||   ||  |    ||  |||     | |         |||   ||| |  ||   |||| |   ||||||||||||||| |||||| ||| |||| |||||||| ||||||||||| |||||  ||
gtaaaaggtgtaaaatagttttgctttaagctgtgatccatagatctttagagtatattttgcctcaatgtccattttggtgactgataattt---tttcatatcagGAAGCACAAATACGCAACGAAAAATATGTCTTGGAAAAGCGCATTGCATATATGCGTCTG

upper sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------gtggctatgcacaataagactcactacattcttttttctactcctttcccaggtatttga--cagcttatgtttcttg---gtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG
                                                              || |  | | |      |  | | || ||  |  ||| |  |  ||| |    ||  | |  ||  | ||   | |||   ||||||||||||||||| ||| |||||| ||||| |||||||||||||||| || |||||  ||
gtaagaaaggggaatgcgatttgatttttttttttcccctttttgttaatcaaacatatgatgttgtcaagtatttcctggatgaatatatcttgatttatttttattttcatattaactaaagcaattcatcgctgttgtttgtagGAAGCACAAATACGCAATGAGAAATATGTTCTGGAAAAACGCATTGCTTATATGCGTTTG

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: 22

GATCTTCTTGCTAAGGTTAAAGAACATGAAGAAGAGATCGCACAGCTCAGAAGGCATCTTGCTGACTACTCTGTGAAGgtggctatgc ... ttcttggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcttttttctactcctttcccaggtatttgacagcttatgtttcttggtagGAAGCACAAATACTCAACGAGAAACATGTTTTGGAAAAACGCATTGCATACATGCGAATG
                             atttgac  putative branch site (score: 22)
                                          tgtttctt  putative PPT
      ttttttcta  TA-rich tract