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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttataaaattcttataatcctgcccaataggcaattcataccattctctccgtagcaagtagaaactgatgtttatccttgttcatcttgttgtagGAACCAGAACAATAGGTGTTTTAAGTAAAATTGATCAAGCATCTGCAGATGCAAAAACTGTATCTTGTGTTCAGGCTATCTTGTCTAACAAGGGTGCACC

Basic information

species Oryza sativa
transcript LOC_Os02g50550.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G163325_T01 (Zea mays), 3'ss of exon 6
gtctgtta-taaaattcttata-atcctgcccaataggcaattcata-ccattctctccgtagcaagtagaaactgatgtttatccttgttcatcttgttgtagGAACCAGAACAATAGGTGTTTTAAGTAAAATTGATCAAGCATCTGCAGATGCAAAAACTGTATCTTGTGTTCAGGCTATCTTGTCTAACAAGGGTGCACC
|||||| | |  |||||    |  |||| | ||| ||      |||| ||| ||||||  || |||        |||| |||   |||||| | || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||| |||||||||||||||| || |||||||||||| | || ||||| || |||||||| ||
gtctgtcactctaattcactcatgtccttcacaacag------catagccactctctcaataccaa-------ttgatatttcctcttgtttaact-gttgtagGAACTAGAACAATAGGTGTCTTAAGCAAAATCGATCAGGCAGCTGCAGATGCAAAAACCGTTTCTTGTGTTCAGTCCATTTTGTCCAATAAGGGTGCCCC
















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: 75 (upstream exon), 57 (downstream exon)
Score: 51

CATAATGATGCAATATTGATTGTTGTGATACCAGCAATGCAAGCTGCTGATGTTGCATCATCTCGAGCTCTCAGACTAGCGAAGGATATTGATCCAGATGgtctgttata ... cttgttgtagGAACCAGAACAATAGGTGTTTTAAGTAAAATTGATCAAGCATCTGCAGATGCAAAAACTGTATCTTGTGTTCAGGCTATCTTGTCTAACAAGGGTGCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctctccgtagcaagtagaaactgatgtttatccttgttcatcttgttgtagGAACCAGAACAATAGGTGTTTTAAGTAAAATTGATCAAGCATCTGCAGATGCAAAAACTGTATCTTGTGTTCAGGCTATCTTGTCTAACAAGGGTGCACC
                      aactgat  putative branch site (score: 51)
                                  tccttgttcatctt  putative PPT
                           atgtttat  TA-rich tract