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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataattccgaagcttgctaatgcatacatttgttgtatccacaaaatatactgatggtcgttgcatatgcttgtgagttgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATACATTTTTTGTTCTCTTCCTACTTATCAGCAGGGAAGACATTTTGTACAAC

Basic information

species Oryza sativa
transcript LOC_Os08g04110.2
intron # 6
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|88519484|gb|CI447138.1|CI447138
EST:     GGTTTTGAACAGATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
genomic: GGTTTTGAACAGATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
EST: gi|86501936|gb|CI144569.1|CI144569
EST:     AGCTTCATAGCACTGAAAGCTGTGAGGTTTTGAACAGATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
genomic: AGCTTCATAGCACTGAAAGCTGTGAGGTTTTGAACAGATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
EST: gi|88283348|gb|CI404794.1|CI404794
EST:     ATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGGCTCTCCTTGGATA
genomic: ATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCA-GCTCTCCTTGGATA
EST: gi|88483042|gb|CI420313.1|CI420313
EST:     TTTTGAACAGATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
genomic: TTTTGAACAGATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
EST: gi|88249832|gb|CI249681.1|CI249681
EST:     AGCTTCATAGCACTGAAAGCTGTGAGGCTTTGAACAGATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
genomic: AGCTTCATAGCACTGAAAGCTGTGAGGTTTTGAACAGATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
EST: gi|88491124|gb|CI428396.1|CI428396
EST:     GATTTTTGAAGAAG                         GAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC
genomic: GATTTTTGAAGAAGgtaatataat ... tgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatccacaaaatatactgatggtcgttgcatatgcttgtgagttgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATACATTTTTTGTTCTCTTCCTACTTATCAGCAGGGAAGACATTTTGTACAAC
               tactgat  putative branch site (score: 2)
       acaaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataattccgaagcttgctaatgcatacatttgttgtatccacaaaatatactgatggtcgttgcatatgcttgtgagttgtgatacagGAGAAATGAGCTCTCGCTTTTCCTTTGAGTTGGTCAGCTCTCCTTGGATACATTTTTTGTTCTCTTCCTACTTATCAGCAGGGAAGACATTTTGTACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA