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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAACATTGAACGATGGAACAAAAAGCGGCAGCAAGCTGTTGACTCCAAAATTGGGCGTCTTGACAAGTTCATTGAACGTGTAAAAGTCCCTATTCAGgtatgctacacatttgttcaaatgcattatgtatctggaatttctgtatatttttaacaatcataaactgaagaaatatactatctataatgatagtcct...

Basic information

species Oryza sativa
transcript LOC_Os01g53560.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53560.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G111510_T01 (Zea mays), 5'ss of exon 12
GTCGAACATTGAACGATGGAACAAAAAGCGGCAGCAAGCTGTTGACTCCAAAATTGGGCGTCTTGACAAGTTCATTGAACGTGTAAAAGTCCCTATTCAGgtatgctacacatttgttcaaatgcattatgtatctggaatttctgtatatttttaa-caatcataaactgaagaaatatactatctataatgatagtcct---------
||| |||||||| || ||||| || ||||| || |||||||||||||||||| |||| || ||||| || || |||||| |||| |||| ||||||||||||||||| || | |||||        || | |||||  ||| |  | |    || ||  ||  |   | | ||||| ||||     |||  |  || ||||         
GTCAAACATTGAGCGCTGGAAGAACAAGCGACAACAAGCTGTTGACTCCAAAGTTGGCCGCCTTGATAACTTTATTGAATGTGTTAAAGCCCCTATTCAGgtatgctgcaaacttgtt--------ttctttatctccaatctgagcagccattcaaataaaaaaggaataaagaagtatatctgttat--ttttattcctgataactga
















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|86505425|gb|CI148058.1|CI148058
EST:     AAATTGGGCGTCTTGACAAGTTCATTGAACGTGTAAAAGTCCCTATTCAG                         GTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCACGATGATCC
genomic: AAATTGGGCGTCTTGACAAGTTCATTGAACGTGTAAAAGTCCCTATTCAGgtatgctaca ... gcacctgcagGTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCA-GATGATCC
EST: gi|88508913|gb|CI436419.1|CI436419
EST:     TCCCTATTCAG                         GTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCAGATGATCCA
genomic: TCCCTATTCAGgtatgctaca ... gcacctgcagGTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCAGATGATCCA
EST: gi|86433513|gb|CI093856.1|CI093856
EST:     AAAGTCCCTATTCAG                         GTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCAGATGATCCA
genomic: AAAGTCCCTATTCAGgtatgctaca ... gcacctgcagGTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCAGATGATCCA

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: 31 (upstream exon), 66 (downstream exon)
Score: 2

GTCGAACATTGAACGATGGAACAAAAAGCGGCAGCAAGCTGTTGACTCCAAAATTGGGCGTCTTGACAAGTTCATTGAACGTGTAAAAGTCCCTATTCAGgtatgctaca ... gcacctgcagGTTTTCATAGCATGTGGTTTAGGGAAAGGAAAAACCTTTCCAGATGATCCATTTCGAAAACCAAACACTGGAATGTGGTGGTTGATGAGAGAGCATTTCA




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