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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacattgcttgttttttattttttgttccctacgagagtgttctattgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC

Basic information

species Oryza sativa
transcript LOC_Os02g17320.3
intron # 14
splice site 3'
intron type U2

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|88254969|gb|CI353793.1|CI353793
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29628991|gb|CB634002.1|CB634002
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|16578897|gb|BI812992.1|BI812992
EST:     TGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCAGGCATC
genomic: TGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGC-GGCATC
EST: gi|86598197|gb|CI354814.1|CI354814
EST:     GATTATCAGTCATCAACACCATTCTTTTTTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGCCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|88262887|gb|CI364465.1|CI364465
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|157650102|gb|EX449736.1|EX449736
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTAAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86505781|gb|CI148414.1|CI148414
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGCCGCCGCCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29622912|gb|CB627923.1|CB627923
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|88273348|gb|CI388804.1|CI388804
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGC---ATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29675419|gb|CB671694.1|CB671694
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|33681231|gb|CF309470.1|CF309470
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29622926|gb|CB627937.1|CB627937
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC
                                   aattgac  putative branch site (score: 3)
                              ataacaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacattgcttgttttttattttttgttccctacgagagtgttctattgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG