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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttccccccttttcatcgacatgatttgttgagcccaatcccaactgctccactaaccctatttgtttaaacttttttccccacttctgtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGGTAAATTGGATTTGAAGAGGACGCAATGCCGAAGATGTTTGGTTTCTCTC

Basic information

species Oryza sativa
transcript LOC_Os11g43590.4
intron # 1
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|88695288|gb|CI737791.1|CI737791
EST:     GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAA                         GAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
genomic: GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAAgtagggcaag ... gtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
EST: gi|88721729|gb|CI745028.1|CI745028
EST:     TTGCTACTGCTGCTGCTCCGATCCAAGAA                         GAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
genomic: TTGCTACTGCTGCTGCTCCGATCCAAGAAgtagggcaag ... gtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
EST: gi|88730451|gb|CI754064.1|CI754064
EST:     AGTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAA                         GAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTACTCATTCCTGTTTTGGG
genomic: AGTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAAgtagggcaag ... gtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
EST: gi|88725142|gb|CI748401.1|CI748401
EST:     GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAA                         GAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
genomic: GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAAgtagggcaag ... gtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
EST: gi|88717759|gb|CI741269.1|CI741269
EST:     GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAA                         GAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG
genomic: GTGTGACCGCTCTTGCTTGCTTGCTACTGCTGCTGCTCCGATCCAAGAAgtagggcaag ... gtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctccactaaccctatttgtttaaacttttttccccacttctgtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGGTAAATTGGATTTGAAGAGGACGCAATGCCGAAGATGTTTGGTTTCTCTC
       cactaac  putative branch site (score: 1)
                            cttttttccccacttc  putative PPT
                tatttgtttaaacttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttccccccttttcatcgacatgatttgttgagcccaatcccaactgctccactaaccctatttgtttaaacttttttccccacttctgtgtttgcagGAGAGAAGAGATTGTGCTAGTAGGGTTTAGTTTAGTCATTCCTGTTTTGGGTAAATTGGATTTGAAGAGGACGCAATGCCGAAGATGTTTGGTTTCTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG