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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagttgtgtacccctaagccaaagtcaataaaatgtccccaatatattattgaatgatactgtgcttatacttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC

Basic information

species Oryza sativa
transcript 13113.m00246
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
gtatgttagttgtgtacccctaagccaaagtcaataaaatgtccccaatatattattgaatgat---actgtgcttatac---ttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC
|||||  |   ||||    ||     ||  | |        |||    | |  | ||  |   |   ||| ||  | ||    || | ||||  | ||| |||||||||||||||| ||||||||||||||  ||||||||||||||||||| ||||| || ||| ||||||| |||||||||||||| |||||||| ||||
gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttgacactttaactttgaatgtatgtttttttaaattgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 5
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 5
gtatgttagttgtgtacccctaagccaaagtcaataaaatgtccccaatatattattgaatgatactgtgctt----atacttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC
||||| ||  |||||    ||     ||  | |      | | | | || |  | |||  ||  ||| ||  |    || | ||     | || ||| |||| ||||||||||| ||||||||||||||  ||||||||||||||||||| ||||| || ||||||||||| |||||||| ||||| || ||||| || |
gtatgctacatgtgttaatcttgattaagatgatct---tctactctattttgttttgtttggcactttggctttgaatgcatacttttttataatttagGGACTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAACTGGTCCTCACATGGTGGTTGCGCCGAAGTCCACCC

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
gtatgttagttgtgtacccctaagccaaagt-caataaaatgtccccaatatattattgaatgat---actgtgcttatacttataaaatcat-cattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC
 |   ||  || | ||   |    |  | ||    |   || |   |||| || | ||||   ||   | | | || | |  |    | || | |   |||||||| || |||||  | ||||| |||||  |  |||| ||||||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||
-tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC

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), 59 (downstream exon)
Score: 59

GTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATGgtatgttagt ... catcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccccaatatattattgaatgatactgtgcttatacttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC
                              ttatacttataaaatc  TA-rich tract