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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacgcttggtgagaagatgatttatttggagatggtggacgacgcctatttctgttttctggctgtctaattctgatgatggcgtctcatgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCGAGCTATTTTGTGTGAAGAAGAAGGATTCCAAGAAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g12950.2
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|88419588|gb|CI686806.1|CI686806
EST:     TTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGCCTCA-G                         GTGCGTTTTGCGTGAAGTGGGTTTCAAGGATGGTTCTAAACCAGGTGCTC
genomic: TTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGC-TCAAGgtacaatccg ... tgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTC
EST: gi|88317369|gb|CI628018.1|CI628018
EST:     TTTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGCTCAAG                         GTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCG
genomic: CTTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGCTCAAGgtacaatccg ... tgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCG
EST: gi|88369555|gb|CI582750.1|CI582750
EST:     CTTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGCTCAAG                         GTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCG
genomic: CTTCCCCGAGGCCGCCGCGGTGGCGGGCTCTTGGGCTGGCTCCGCTCAAGgtacaatccg ... tgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttctgttttctggctgtctaattctgatgatggcgtctcatgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCGAGCTATTTTGTGTGAAGAAGAAGGATTCCAAGAAGAAAG
                          ttctgat  putative branch site (score: 3)
                                             tgtttttc  putative PPT
                                            atgttttt  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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacgcttggtgagaagatgatttatttggagatggtggacgacgcctatttctgttttctggctgtctaattctgatgatggcgtctcatgtttttcagGTGCGTTTTGCGTGAAGTGGGTTTTAAGGATGGTTCTAAACAAGGTGCTCGAGCTATTTTGTGTGAAGAAGAAGGATTCCAAGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA