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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaatatctctagtgcttattgtatacactaaatataccatatgagtgaccacttctgactgaccctattcgcacaaaatgattgacatggcggttttatacatattattattttctgataaagatacatattattattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGGTCGCTCATCAGCTTGGACACTAAAGATGCAAGTCCATCAAGCTCCCCAG

Basic information

species Oryza sativa
transcript LOC_Os05g01240.2
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|86256680|gb|CI061443.1|CI061443
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|29625695|gb|CB630706.1|CB630706
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|33381398|gb|CF196741.1|CF196741
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|29674666|gb|CB670941.1|CB670941
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|88902803|gb|CI088341.1|CI088341
EST:     ACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: ACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|86854490|gb|CI256612.1|CI256612
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|88840608|gb|CI080062.1|CI080062
EST:     TTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: TTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|88268876|gb|CI377780.1|CI377780
EST:     ACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: ACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|29674667|gb|CB670942.1|CB670942
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
EST: gi|29678624|gb|CB674899.1|CB674899
EST:     GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAG                         GAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG
genomic: GGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatat ... attattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcggttttatacatattattattttctgataaagatacatattattattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGGTCGCTCATCAGCTTGGACACTAAAGATGCAAGTCCATCAAGCTCCCCAG
                         ttctgat  putative branch site (score: 3)
      ttttatacatattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaatatctctagtgcttattgtatacactaaatataccatatgagtgaccacttctgactgaccctattcgcacaaaatgattgacatggcggttttatacatattattattttctgataaagatacatattattattgcagGAGCCTTTTCCTGTGGGGAACAATGTCCGGTCTAGGGCTGGGAGAAATAGGTCGCTCATCAGCTTGGACACTAAAGATGCAAGTCCATCAAGCTCCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT