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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtcctggatatttctcattgtgtaactatactccttttactagctaaaggaataaaaagtatctgaaatcttatctttgtacttttccttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG

Basic information

species Oryza sativa
transcript LOC_Os12g13130.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 7
----------aggtcctggatatttctcattgtgtaactatactccttttactagctaaaggaataaaaagtatctgaaatcttatctttgtacttttccttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG
          | | ||  || |    ||  |  | ||  |||||  | |  ||   || | |   | || | |  |  |||  |||     |   |   ||||| ||||||||||||||||||| || ||||| |||||||     || ||  |  |||||||||| ||||||||||| || || ||| ||||||||||
agcttcatcaatggcccagaaaaaaatc-ctaggaaaagatacttatat--cttaatagaagttcagaagggactt--aatgctat-----tgtctgctcttttctgcagAAACAAACAAACAGGTTATACCTCGCTCTCTCCATTTTGACGCTGATACTTTTGCCGCTGTTCTATCTAATTGTGTTCCTGCACCAGAG
















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|88690274|gb|CI734353.1|CI734353
EST:     ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGG                         AAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
genomic: ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGGgtgagagaat ... ttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
EST: gi|88688437|gb|CI732013.1|CI732013
EST:     ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGG                         AAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
genomic: ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGGgtgagagaat ... ttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
EST: gi|29645805|gb|CB650812.1|CB650812
EST:     ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGG                         AAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
genomic: ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGGgtgagagaat ... ttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
EST: gi|29645769|gb|CB650776.1|CB650776
EST:     ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGG                         AAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
genomic: ATGCCCACACATGCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGGgtgagagaat ... ttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
EST: gi|88222581|gb|CI222537.1|CI222537
EST:     GCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGG                         AAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT
genomic: GCAAGAATGGCTCTAAACCTTTCCCCAAAGGTGGCAGGgtgagagaat ... ttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaaggaataaaaagtatctgaaatcttatctttgtacttttccttttgtgcagAAACAAACAAACAGATTCTACCTGGCTCTCTGTGCCTTAACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG
 agctaaa  putative branch site (score: 3)
                         tcttatctttgtactt  putative PPT
       aataaaaagtatct  TA-rich tract