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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcttctttgacatttaagttgttgtacactgtcatcacaagcatccaactttgcaagtgtttttgttataaataactttttcccctatctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATAGCTAATAACCCGCTAAGCATCAGAACACATGAAATCGGTAAGCGCCACA

Basic information

species Oryza sativa
transcript LOC_Os06g11170.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g11170.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G080120_T02 (Zea mays), 3'ss of exon 1
catcttctttgacatttaagttgttgtacactgtcatcacaagcatccaactttgcaagtgtttttgttata-aataa---ctttttcccctatctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATAGCTAATAACCCGCTAAGCATCAGAACACATGAAATCGGTAAGCGCCACA
    |   ||| |  ||| |||||| |||  |||  |   || ||||||  | ||||| |    |||    | |||||   || |||  |||  ||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| || ||  |  | |||||||| ||||||||| | |||||||||||||
----tctgttggctcttatgttgttatactatgttgtaggaaacatccatttgtgcaaattcgcttggggaataataagttctcttttgcctcccttgtttcagTATTGGGTGAGCCAAGGAAACAAATGGTGCGACTTCTGTAAGATTTATATAGCAAACAATTCCTTCAGCATCAGGACACATGAACTTGGTAAGCGCCACA

upper sequence: LOC_Os06g11170.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G49590.2 (Arabidopsis thaliana), 3'ss of exon 1
------------catcttctttgacatttaagttgttgtacactgtcatcacaagcatccaactttgcaagtgtttttgttataaataactttttcccctatctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATAGCTAATAACCCGCTAAGCATCAGAACACATGAAATCGGTAAGCGCCACA
               | |||||    |  || |   | |  | |   |  ||     ||    || | || ||   ||| | |   | | ||| |    | | || || ||||| ||||| || ||||| |||||||||||||| ||||||||||| |  |||   || || ||   ||| || ||||  |||||  | |||||||| ||| 
gtaaatcaaaattcgcatcttttctctccaaatctctttgaattacgaa-acctctgtcttgtttcgtaattgaaattgatct---tgagtttgttttttgtgttatttcagTATTGGGTAAGTCAAGGGAACAAATGGTGTGAATTCTGTAAGATATGGATACAGAACAATCCAACAAGTATTAGAAACCATGACCTTGGTAAGCGTCACC

upper sequence: LOC_Os06g11170.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0063g00890.t01 (Vitis vinifera), 3'ss of exon 1
----catcttctttgacatttaagttgttgtacactgtcatcacaagc--atccaactttgcaagtgtttttgttataaataactttttcccctatctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATAGCTAATAACCCGCTAAGCATCAGAACACATGAAATCGGTAAGCGCCACA
        || ||| ||||||    |||| |||| |        |  |  ||   | | |    || | | |  | ||  |||| |||  ||     | ||| ||||||||||| ||||| || |||||||||||||||||||| || || || ||||| || || ||    ||||| ||||  |||||| | ||| | |||||||
tgtcttatttatttaacatttctcctgtt-tacagTACTGGGTTAGCCTGATTTTATTGTTTGTGTATGTCTTATTTATTTAACATTTCTCC-----TGTTTACAGTACTGGGTTAGCCAGGGTAACAAATGGTGTGACTTCTGCAAAATCTATATAGCCAACAATCCTTCTAGCATTAGAAACCATGAACTTGGTCAACGCCACA

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|88734451|gb|CI757959.1|CI757959
EST:     ACTGTCGCAATCGGNGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88300055|gb|CI580116.1|CI580116
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TAGTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88721217|gb|CI744516.1|CI744516
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88719760|gb|CI743270.1|CI743270
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88412078|gb|CI566807.1|CI566807
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88727406|gb|CI751061.1|CI751061
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88827910|gb|CI778475.1|CI778475
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88760243|gb|CI769799.1|CI769799
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88734663|gb|CI758171.1|CI758171
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|218505040|gb|FG968804.1|FG968804
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88828056|gb|CI778621.1|CI778621
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88695704|gb|CI737742.1|CI737742
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88314033|gb|CI600035.1|CI600035
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88734817|gb|CI758325.1|CI758325
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
EST: gi|88733714|gb|CI756891.1|CI756891
EST:     ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAG                         TACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA
genomic: ACTGTCGCAATCGGCGCAGCTGAGCGGAGCCCTTGCCCGCCATGACGGAGgtacgctctc ... ctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaactttgcaagtgtttttgttataaataactttttcccctatctttttccagTACTGGGTGAGCCAAGGAAACAAATGGTGTGACTTCTGTAAGATTTACATAGCTAATAACCCGCTAAGCATCAGAACACATGAAATCGGTAAGCGCCACA
                          aaataac  putative branch site (score: 2)
                             taactttttcccctat  CT-rich tract
           aagtgtttttgttata  TA-rich tract