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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatggataatttaattgttattattggaatttaactctctccatgctatggtgattttactaatatatttgggagtcctgcgctaagaggttaatctgttgctttgggttctttttagGATTTGCCTAGAACGTTCCCAGGTCATCCCGCACTAGATGAGGATGGCAGAAATGCTTTAAGACGCTTGCTCACAGCTTATGCGAGACATAACCCATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g61860.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 4
gtagatggataatttaattgttattattggaatttaactctctccatgctatggtgattttactaatatatttgggagtcctgcgctaagaggttaatctgttgctttgggttctttttagGATTTGCCTAGAACGTTCCCAGGTCATCCCGCACTAGATGAGGATGGCAGAAATGCTTTAAGACGCTTGCTCACAGCTTATGCGAGACATAACCCATCAG
                                          |  ||   ||  | |||||   |     ||  | | || |  | | |       || | || ||||||     |||||||||||||||||||| || ||||| || || |||||||||||||||||||||||||| ||||| ||||||||||||||||||||  |||| || ||| |||
-----------------------------------------gtatatatcatttt-attttttaaccgggttctgtattcatttgttgatg---ccatttcttactttggaac--ttttagGATTTGCCTAGAACATTTCCAGGACACCCTGCACTAGATGAGGATGGCAGAAATGCCTTAAGGCGCTTGCTCACAGCTTATGCTCGACACAATCCACCAG

upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 4
gtagatggataatttaattgttattattggaatttaactctctccatgctatggtgattttactaatatatttgggagtcctgcgctaagaggttaatctgttgctttgggttcttttt--agGATTTGCCTAGAACGTTCCCAGGTCATCCCGCACTAGATGAGGATGGCAGAAATGCTTTAAGACGCTTGCTCACAGCTTATGCGAGACATAACCCATCAG
           || |  || | ||  ||     |||    |||  || || || |  | ||  ||  |   ||   |    |    |   ||  || ||  ||    | | || |||    ||||| ||||| |||| || || |||||||| || || || |||||||| ||||||||||| ||||| || || || || |||||  |||||||||| ||||
---------gtatatgcttttgatatttcacccttattgttcttaatactgtgatattattggtatgactctttaaacaagtttcttcttag--tagtccattatcattgcttgtttgcgcagGATCTGCCTCGAACATTTCCTGGTCATCCTGCTCTGGACGAGGATGGTAGAAATGCTTTGAGACGATTACTTACTGCATATGCTCGACATAACCCCTCAG

upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 4
gtagatggataatttaattgttattattggaatttaactctctccatgctatggtgattttactaatatatttgggagtcctgcgctaa-gaggttaatctgttgctttgggttctttt--------------------------tagGATTTGCCTAGAACGTTCCCAGGTCATCCCGCACTAGATGAGGATGGCAGAAATGCTTTAAGACGCTTGCTCACAGCTTATGCGAGACATAACCCATCAG
||   |  ||   |    | | |   || | | | || |   |  ||  |  |||| |     |  || ||     | ||    |  |  |    |||||| |   |   || | |  |                           ||||||||||| |||| |||||||||||||| || |||||||||||||| ||||||||||| || || || || || || |||||  |||| ||||| || |
gtcattacatgcatatgctttgaaatttagtactcaatttctttgattttcaggtgttgcctttgttaaatccaaaaatctcaagtcattgttactaatctctaaatgcaggatttactgatcaaaaaaaaaaaatttctaaatgcagGATTTGCCTCGAACATTCCCAGGTCATCCTGCTCTAGATGAGGATGGTAGAAATGCTTTGAGGCGTTTACTTACGGCATATGCTCGACACAACCCCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttgggagtcctgcgctaagaggttaatctgttgctttgggttctttttagGATTTGCCTAGAACGTTCCCAGGTCATCCCGCACTAGATGAGGATGGCAGAAATGCTTTAAGACGCTTGCTCACAGCTTATGCGAGACATAACCCATCAG
                         ggttaat  putative branch site (score: 4)
                                             ttcttttt  putative PPT
                                             ttcttttta  TA-rich tract