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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG

Basic information

species Oryza sativa
transcript LOC_Os05g02670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
gtgagtaaacttaaaattttctattcattgattaaaatat--aatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
|||||| |  |  |||| | | ||| || ||| |||| ||  |||   ||| |||||| |||||| |     | |  |||| | | || ||||   |||||||||||||||||||||||||||| |||||||||||||| ||||| || |||||||| || || |||||||| || || |||||||||||||| ||||||||
gtgagttacttctaaatgtccaatt-atagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G40580.1 (Glycine max), 3'ss of exon 5
gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttca-actgcccaata-ctacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
     |  |||       || | |      | |    |   || | |||     |      | |  ||   ||| || |  |    |    |  ||  |||||||| ||||| || |||||||||||||| ||||| |||||||| |||||||| ||||| || ||||| || ||||| ||||| || ||||| ||||| ||
----tttcactgctggcattatctctgcctagttctgtggcatttgtctggggaaaaaaaaacatagctttatagcttcactaagaagaagaaaatacttgcagGGTAGAGCAAGGGAGGCTGGGGAGATAAACAAAAGCTTGCTTACACTTGGACGAGTGATTAATGCGCTAGTTGAGCACTCAGGTCATGTTCCATATAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G15520.2 (Glycine max), 3'ss of exon 4
gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatca--------ttgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
         | | |  |||      |  ||||||   |  | ||| | | |   |    | || ||    |||    |||||| ||| | || | |        | |||||| ||||| || || ||||||||||| || || |||||||| |||||||||||||| || |||||||| ||||| || || || ||||| || || ||
--------gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgtt--atagcttttttgagattcatttgtaagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTCTAGTTGATCATTCAGGTCATGTGCCTTATAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 4
gtgagtaaacttaaaattttcta-ttcattgattaaaatataatatatctatc-tgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
 |   |    | |    |  ||| |||  | |      | |   | |   ||| |   |||  | || | | |           ||| |   |     |||||||| ||||| || |||||||||||||| || || |||||||| |||||||| ||||| || |||||||| ||||| ||||| || ||||| ||||| ||
-ttgctggcatcatctctgcctagttctgtcacatttgtctggaaaaaaaatcatagctttagagcttcactaagaagaagaaaatact---tggcacttgcagGGTAGAGCAAGGGAGGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGACGAGTGATTAATGCTCTAGTTGAGCACTCAGGTCATGTTCCATATAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G07910.1 (Glycine max), 3'ss of exon 4
gtgagtaaacttaaaatt-ttctattcattgattaaaatataatatatctatctga--tttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
  |  | | ||| |  |   |||  | |||  | |  || |     |     || |  | ||  | ||        || | ||||   |   |  ||  | |||||| ||||| || || ||||||||||| || || |||||||| |||||||||||||| || |||||| | ||||| || || || ||||| ||||| ||
--gcattatctttatctcactctgattattcttcagtatttgtctgaaaagactaaaatgttatagcttttttgagcttcatttg---taagaaaatgctcgcagGGTAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGTCGAGTGATTAATGCTTTAGTTGATCATTCAGGTCATGTGCCATATAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtgagtaaacttaaaatttt--ctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
     | |   |      ||   |   | || |||||   ||  ||| | | |     ||||  || | ||   |||||  |   |   ||||         |||||||| ||||| || || ||||| ||||||||||| || ||||| |||||||| || ||||| |||||| | |||||||||||||| ||  | ||||| ||
gtacctaaaacagtcaggaaccatgattttttattgacagaataatagtgtcttaccttgatgattta-ctaaacaatataagagtcactatt---------ttgcagGGTAGAGCCAGGGAAGCTGGTGAGATCAACAAAAGTTTGCTCACACTTGGACGTGTCATAAATGCTTTGGTTGAACACTCTGGTCACATTCCATATAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
    ||| ||||   || || |  |||| |  |   |  | |  | |||  | |    |        | | | |||    |  |    || | | |||||||||  |||| ||||| ||||| |||||||||||||| || || || ||||| || ||||| || || ||||| || |||||||| ||| | || |||||
----gtatacttt--atcttattatcatcgtctctgaggtca-gtgtcttccaggcagtcatggaagctagtgctaagcattttgac-aactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG

upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 5
-----gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
        || | |   | ||| |    ||  |   |||    || | |  |  || |   ||  ||       | |   |||    | ||| |||     || ||||||||||| || || ||||||||||| || || |||||||| || ||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||
acaacaaaagcatatgcataatatgaagtt-gtgtgttaggcaatgaaaagttcatttatcttcacataaa---agtttgactgcaaaaattcaatgc---tttcagGGCAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACTCTTGGGCGTGTTATTAATGCGCTGGTTGAGCACTCTGGTCATGTTCCATATAG

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|58664623|gb|CK053309.1|CK053309
EST:     TAGTCGATCTAGCTGGTTCAGAAAATATCTCACGGTCAGGTGCTAGAGAT                         GGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGT
genomic: TAGTCGATCTAGCTGGTTCAGAAAATATCTCACGGTCAGGTGCTAGAGATgtgagtaaac ... atcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
                              ttttgat  putative branch site (score: 4)
                              ttttgatattgaatta  TA-rich tract