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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaaaagaaaaactgaattccttattttaattccaatataactagagttgccaggaatatttatttgattgtcaacactgcag

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 5'ss of exon 15
GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaaaagaaaaactgaattccttattttaattccaatataactagagttgccaggaatatttatttgattgtcaacactgcag
 || ||||||||| ||||||| |||||||||||||||||| | |||||||| |||||  ||||||| || |||||  | || || |||||  | ||||||||    |||    ||||   |  ||     || || | || || | ||  ||   |   || | |||||| |  |   | |     
ATCAAACATGCCTGACGGGCAACCAAAATGGCTTCTCTCTATTATTCCGGGATACCCTATGCTCAATTTCATGCTGACAACTGCTATATACGTCCTTgtaag----aaaccgtaacttcttctctccccgtattttctat-tagcaagctttctgaaacatctctatttgttcttgttcgccag--
















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|86885457|gb|CI318608.1|CI318608
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88995453|gb|CI022776.1|CI022776
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88513138|gb|CI440644.1|CI440644
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88502372|gb|CI429878.1|CI429878
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88477010|gb|CI414281.1|CI414281
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88560911|gb|CI491614.1|CI491614
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTTTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88322184|gb|CI537767.1|CI537767
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88846659|gb|CI373427.1|CI373427
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88515591|gb|CI443245.1|CI443245
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|86498852|gb|CI141485.1|CI141485
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|89177189|gb|CI043692.1|CI043692
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88517436|gb|CI445090.1|CI445090
EST:     GGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCGTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTAT
genomic: GGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTC-TTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTAT
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88956170|gb|CI092458.1|CI092458
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
EST: gi|88507120|gb|CI434626.1|CI434626
EST:     CGGGTTACCCACTGCTCAACTTTATGCTTGGTACAGCAATATATCTTCTT                         ATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT
genomic: CGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATT

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: 59 (upstream exon), 73 (downstream exon)
Score: 18

GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTTgtaagtaaaa ... aacactgcagATATCATACAGAGTGTTTGAGCTGACAGGTGTGTTGAAGTCAGCTTTTATTCCCAGCAGAGATAACAATCGTCTATATCAAAATTTTGTTGCCGGGATTG




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