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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
agtcatatgcct-tctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactgtataaattcat-ctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
  ||   |   | |||      | |    ||| ||    ||   |  |    | |   |||   ||    ||| | | |  |||  |  | | ||  |||||||||||||| |||||||||||||||||||| ||| | ||||| ||||||||||||||||||||||||||||| || |||||||| || |||||||| || 
-ttcggttatttctctgcgcgctgtgctatttttaccgaataagttgaaccttttcccacc-tagtgaaaactttgtgatctcacacgtatgcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactgtata-----aattcatctcacgtttaat----gcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
     ||||  | | |||    || |  |       |  || |   | |       | ||  ||  |    ||| |      ||||   |   | ||| ||    |||| |||||| | ||||| || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||||| || || || ||||||||||||
----gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
---------agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactg----tataaattcatctcacgt--ttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
         | |||    | ||  || | | | ||| |   | | | |  |    |||  | ||  |    | |  |  |||    | | | |  |  |||     | | | ||| |||||| | ||||| || ||||||||||||||  |||| || ||||||||||||||||||||||||||||||||||| || || |||||||||||||||
gtatgttccaatcagtaacttttgatgttaaa-atattccatgt-tgagagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 5
---------agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactg----tataaattcatctcacgt--ttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
         | |||    | ||  || | | | ||| |   | | | |  |    |||  | ||  |    | | ||  |||    | | | |  |  |||     | | | ||| |||||| | ||||| || ||||||||||||||  |||| || ||||||||||| ||||||||||||||||||||||| || || |||||||||||||||
gtatgttccaatcagtaacttttgatgttaaa-atattccatgt-tgagagaagaaggggtattctagtgttatgctgtctgcttgtctgactgaacttcattgcatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCTAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
agtcatatgccttctata--tcatatatagtttgtatgtc--attgttctaggtctgttgaaccactgtactcactgtataa--attcatctcacgtttaat--------gcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
     ||||||| | |||  | || |   | | | ||||   |   |   | |       |  |  ||  ||   |||||     ||  | | || || | |        |||| |||||| | || || || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||||| || || || ||||| ||||||
----gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
agtcatatgccttctatatcatatatagtttgtatgtcattgttct----aggtctgttgaaccactgtactcac-tgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
      |||||||  |   ||| ||     |     |  ||||  |    |  | | ||     | |||  ||   | | |     || |   |    | ||||| |||||||| || || || |||||||||||||| ||||| || || ||||| |||||||| |||||||||||||| || || ||||| ||||||||||||
-----gatgcctttaaaggcatgtacttcctcataatttttgtggtgaaaaaatttatttgtttaatgtgttcttgtttgtctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------agtcatatgccttctatatca---tatatagtttgtatgtcattgttctaggtctgttgaaccactgtactc----actgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
                                                                |  ||| |  |  |||||||    | |  |  ||||  || | |||| ||| |  ||  |     ||| ||     ||| ||| | || ||   |    |  ||||| || || || ||||||||||| || || |||||  ||||||| || |||||||| ||||| || ||||||||||| || ||||| || ||||| || || 
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtg-gtaactgttttagctaggtaaagtggatgtgcttcttaactttattagtt-ataatatacctg-tgcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------agtcatatgcctt-ctatatcatatatagtttgtatgtcattgttctaggtctgt---tgaaccactgtactcactgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
                                                                                                   | | |  |  || ||  |  ||  | ||   | |  | ||  ||  | |   ||   |    |    |  | ||| | |   | |||   |    |  ||||| || ||| | |||||||| || || || ||||| ||||| || || |||||||| || ||||| ||||||||||| |||||||| || ||||| || || 
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcga-aggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggt-cataatatacatg-tgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58603359|gb|CK013887.1|CK013887
EST:     CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG                         TGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
genomic: CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcact ... tttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG                         TGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
genomic: CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcact ... tttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG                         TGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
genomic: CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcact ... tttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     CTAGGGGATCAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG                         TGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCC
genomic: CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcact ... tttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCC
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG                         TGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA
genomic: CTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcact ... tttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggtctgttgaaccactgtactcactgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT
                            tataaattcat  TA-rich tract