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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcgcatcttcttgattatctttattaaaacaataggcttttaggaggttcccgtttgatgtgctgatggctgttgtatttttattttaaatctgtgataatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAAGACATATCTGGTGTCCGAATTGGCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g46740.2
intron # 4
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|58672683|gb|CK061369.1|CK061369
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|218505243|gb|FG948331.1|FG948331
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|58693740|gb|CK082427.1|CK082427
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGA
EST: gi|88413348|gb|CI581363.1|CI581363
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|29620621|gb|CB625632.1|CB625632
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|58693286|gb|CK081973.1|CK081973
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACA
EST: gi|226698432|gb|GO497010.1|GO497010
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|218486282|gb|FG952873.1|FG952873
EST:     GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
EST: gi|58592609|gb|CF990917.1|CF990917
EST:     GAAAGTCAACTGTTTAGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG                         GGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA
genomic: GAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAGgttatcgcat ... taatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatgtgctgatggctgttgtatttttattttaaatctgtgataatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAAGACATATCTGGTGTCCGAATTGGCTTG
        tgctgat  putative branch site (score: 3)
                    ttgtatttttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcgcatcttcttgattatctttattaaaacaataggcttttaggaggttcccgtttgatgtgctgatggctgttgtatttttattttaaatctgtgataatgagaagGGCGATGTTATTATTTGCGGAAGAAAAAGACATGGGCTAGTTAGTGATGAAGACATATCTGGTGTCCGAATTGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA