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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttttaaatatcctttttgaatttctgtactttcaccatacaaagtttctgttaaggtattctaaaatatttttatttgaatgctcattctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA

Basic information

species Oryza sativa
transcript LOC_Os01g34480.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34480.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179981_T01 (Zea mays), 3'ss of exon 3
tccttttaaatatcctttttgaatttctgtact--ttcaccatacaaagtttctgttaaggtattctaaaatatttttatttgaatgctcattctgctt--cagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA
       |||      |||     |  | |||   |    ||  | |  ||  | || |  |  ||     || |||  | |  | |   |  ||  ||  |||||||||||| || |||||||||| || ||||||||||||||||||||||| ||||  ||||||||| ||||||| |||||  | |||||||| ||||| |
----agcaaagtctgatttcattgtcttataccaatgtctcaagctatattgttatttattttatcattgctactttattctctaagtctacactatttggcagCAATGGTATATTTTGTCCAAGACGCTGGCAGAGGAGGCTGCTTGGAAGTTCTCAAGGGATAATGGACTTGAAATCGTTACTATAAACCCAGCGATGGTTA
















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|568053|gb|D38888.1|D38888
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|29640618|gb|CB645627.1|CB645627
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|29616459|gb|CB621471.1|CB621471
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|117221000|gb|CT845506.1|CT845506
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|11026105|gb|AU162706.1|AU162706
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAACAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|2312785|gb|C28940.1|C28940
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|84117052|gb|CD150819.1|CD150819
EST:     TTGTTGATGAGACATGGGGTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTATCAGAGGAGGCTGCTTGGAA
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctgttaaggtattctaaaatatttttatttgaatgctcattctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA
                ttctaaa  putative branch site (score: 2)
                                            ttctgcttc  putative PPT
        ttaaggtattctaaaa  TA-rich tract