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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttgttgaaatcaattgtgtgtttgaaagcatgcagagtattacaataagtaaacttgcagccattggttgaatcaattgtgtgtttgggcatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g09550.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G117388_T01 (Zea mays), 5'ss of exon 3
ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgta------agtcttgttgaa-atcaattgtgtgtt--tgaaagcatgcagagtat-tacaataagtaaacttgcagccattggttgaatcaattgt---gtgtttgggcatgcag
|||||||||||||| ||||| |||||||||||||     ||||| || || ||||| ||||||||||||||||||||      ||| ||| |||  |   ||| |    |  ||| ||  |    | ||| || |||  ||||| | ||     ||| ||| ||    | |   |||||| |||||||||
ATATGGAGGCTATTGACAAGTTTCTTTTTCCTGGCACCATTTTCCATGAAATTTGGTATTCGCCTTCTGATGATgtaggttaaagttttgctgactactgattataaaatagtgacagt-tatgaactatctataatt-gtaaattagctttggttgtttggatttgctttatcgtgttttggcatgcag

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143817_T01 (Zea mays), 5'ss of exon 3
ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttgttgaaatcaattgtgtgtttgaaagcatgcagagtattacaataagtaaacttgcagccattggttgaatcaattgtgtgtttgggcatgcag
 |||||||| |||||||||| ||||| ||||||||    ||||| || |||||||| |||||||||||||||||||||||     |       |       |   |||  |||   | |   ||| ||  || | ||  |      | | |  |   |    | | |  ||||    
GTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatag--
















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|29671730|gb|CB668005.1|CB668005
EST:     TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
genomic: TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
EST: gi|27578253|gb|CB000948.1|CB000948
EST:     TTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
genomic: TTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
EST: gi|218492921|gb|FG948483.1|FG948483
EST:     TTTTCCTGGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
genomic: TTTTCCT-GGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
EST: gi|157651306|gb|EX450940.1|EX450940
EST:     TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCACCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
genomic: TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
EST: gi|58692377|gb|CK081064.1|CK081064
EST:     TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGG
genomic: TTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGG
EST: gi|27554498|gb|CA998398.1|CA998398
EST:     TTTTCTATCAACTTTGGGATTCGCCTTCTGATGAT                         AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC
genomic: TTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 71 (downstream exon)
Score: 60

ATATGGAGGCTATTTACAAGCTTCTTTTTCCTGGGCAAGTTTTCTATCAACTTTGGGATTCGCCTTCTGATGATgtaagtcttg ... gggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG




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