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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTATCGACGAGGTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGA

Basic information

species Oryza sativa
transcript LOC_Os06g50050.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G158136_T01 (Zea mays), 3'ss of exon 2
gtcagctccgcgcgcaaatccttcggtttaactgccgc-----------tccttttcatttgtttgttgtt--atcgctgctgatttatgaaacatcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTATCGACGAGGTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGA
   ||||| || |  |  | ||    |  || ||  ||           |  ||||    ||| || | |   |  | || || | | | |    | | |||||| ||||||| ||||||||||| |||||||| ||||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||| ||||| ||
---agctctgcacatatttactaatttagaattgatgccaactgtattgttttttttgcgtgtatgctatacaactgatgttggtatgttattgctgtggcagTGGCTGCTGTCTTTAGTCTCGCTCACAAGCTCCAGCCTGCTATTATCTTCATTGACGAGGTCGACAGTTTCTTGGGGCAGCGACGGACAACTGACCATGA

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G075584_T02 (Zea mays), 3'ss of exon 2
----gtcagctccgcgcgcaaatccttcggt-ttaactgccgctccttttcatttgtttgt-tgttat-cgctgctgatttatgaaacatc----ttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTATCGACGAGGTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGA
     ||  || |    | |      | | | | | |||       |||| || ||| | |  | ||| ||||| || ||  ||    ||     | |||||||||||||||||||||||||| |||||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||||||||||||| || || ||
acatatctactactttagaattagaattgatgtcatctgtattgtttttttatgtgtgtctacgctatacgctgatg-ttagtgtgctattgctgtggcagTGTCTGCTGTATTTAGTCTCGCTCACAAGCTCCAGCCTGCTATTATCTTCATTGACGAGGTTGATAGTTTCTTGGGGCAGCGACGGACAACTGATCATGA

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0098g01260.t01 (Vitis vinifera), 3'ss of exon 2
-----gtcagctccgcgcgcaaatccttcggtttaact------gccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTATCGACGAGGTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGA
     |  |  |  |     || |  ||   ||   ||       || || |      ||| | | ||| | |    | |||| | |   | |   ||||||| |||||||||||||  | ||  |||| || || || ||||||||||| || || ||||| |||| ||| ||||| ||||| |||||||| ||||| ||
ttgttgaaaatttggttgtaaagttgtttaattggtcttgttttaccactaccaagtgtttctct-ttgatctgaacgttgatcttttctaaactctgcagTGGCTGCTGTATTTAGCTTGGCTTACAAACTCCAACCTGCTATTATCTTCATTGATGAGGTTGATACTTTTTTGGGTCAGCGCCGGACAACAGACCATGA

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|218492085|gb|FG945532.1|FG945532
EST:     TCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: TCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|218479629|gb|FG945760.1|FG945760
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|218505299|gb|FG958827.1|FG958827
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|29622367|gb|CB627378.1|CB627378
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|33654383|gb|CF276997.1|CF276997
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTATCGACGAGGTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGA
                              tgctgat  putative branch site (score: 3)
                                   atttatgaaa  TA-rich tract