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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttaatacaagttaattgctttctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgttgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC

Basic information

species Oryza sativa
transcript LOC_Os01g58114.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 1
-ttcttaatacaagtt-aattgctttctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgtt---gcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
  |   | |  || || | |    |||||     ||  | || ||| | |     | ||| | ||   | | | ||| ||   |  |  ||      |   |||||||  |||||| || ||||||||||||||||| || ||||| ||||||||||||||  | ||||||||||||||||||||| | || || ||||| || |
tcttgcagtgtaatttcagtaaaattctg----ctcctaattttctgcgcggttgttttcct-ttgccttaatgttggtctaaaatcgattataaacttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G54870.1 (Arabidopsis thaliana), 3'ss of exon 1
----ttcttaatacaagttaattgctttctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgttgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
     |  |  || ||| | ||    |||| ||   |  ||      |    ||   | || || || ||  | |  | |   |||   ||||  || | | || |  | || || ||||| ||||| || || || |||||||| |||||||| ||||||||||||||||||  ||  |||||  |    ||  |||||||  
gtggatactcttagaagatgatg--cttcttaattcttacacaaagttttggatttttttttttttttttgtatt-ctaagtttgattatgttgtttat-gaagGCGGATAAGGCACATAGTTGGACATGTATGGATCTTTATGTATTTGCAACTCCATATCGTGTTACATGGACTTGGTACTTCATTTCACGACAGCATACTG

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G27020.1 (Arabidopsis thaliana), 3'ss of exon 1
ttcttaatacaagttaattgctttctgaaggttctcatttctctacacat--gaa--tattcttcttat------ttcactattgatcctgacactgttccttgt-tgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
           |   ||||     || |  |||    || |||| ||| |  |||  | || |||  ||      | |   |||||| |||         ||| | |||||    | || || ||||| ||||| ||||| ||  ||||||| ||||  |||||||||||||| ||||||||||  |||||||      | ||||| ||  
-----------aaaaaattataggcttagagttacatttcctcttcaccttggaagctgtttttcgaatgatgaatacttaattgattctgttgaaacgtcttttgtgcagGTCGATAAGGCACATAGTTGGACGTGCATGGATATTTATGTCTTTGTCACACCATATCGTGTGACATGGGATTGGTACTTTGCTTCGAGAGAGCACACTA

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0090g00130.t01 (Vitis vinifera), 3'ss of exon 1
ttcttaatacaagtta-attgcttt--ctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgttgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
   |  |  |   ||  |||  | |      |    || || |  | |  ||  |  ||   |  | |||  || |  |     || || || |||||| |||   |  |  || ||||| ||||| || || ||||||||||| |||||||| ||||| |  || |||||||||||||||||| |   ||| ||||||||| 
gcttggaagcttcttgtattagtataatcatataccctaatatggcca-gcagaagaatagattatttttagctttaaaatgctactct-ttacttgtt-cagGTTAGTAGTGCCCATAGTTGGACATGTATGGACCTTTATGTCTTTGCAACTCCATACCAAGTGACATGGGATTACTACTTTTTGTCTCGGGAGCATACCA

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0090g00100.t01 (Vitis vinifera), 3'ss of exon 1
ttcttaatacaagtta-attgcttt--ctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgttgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
   |  |  |   ||  |||  | |      |    || || |  | |  ||  |  ||   |  | |||  || |  |     |  || || |||||| |||   |  || || ||||| ||||  || || ||||||||||| |||||||| ||||| |  || |||||||||||||||||| |   ||| ||||||||| 
gcttggaagcttcttgtattagtataatcatataccctaatatggcca-gcagaagaataaattatttttagctttaaaatgctattct-ttacttgtt-cagGTTAGTAATGCGCATAGTTGGAAGTGTATGGACCTTTATGTCTTTGCAACTCCATACCAAGTGACATGGGATTACTACTTTTTGTCTCGGGAGCATACCG

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 2
-----ttcttaatacaag--ttaattgctttctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgt-tgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
      || ||     |   || |    ||| || | |   || | | ||    ||| | ||        | |||| |  ||||  |    | ||| | ||| |||||||||  |  || || |||||||| ||| |||| ||||| || |||||||| ||||| ||||| || |||||||||||||||   | |||  | || || |
tgttactcatagctttaaccttgacaattttatgcaagcg-tcgtctttcatgtcataatta-------caattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgaatattcttcttatttcactattgatcctgacactgttccttgttgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC
                               tcctgac  putative branch site (score: 2)
                                       ctgttcctt  CT-rich tract
      aatattcttcttattt  TA-rich tract