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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactttagcttttgtcattctaatgttaacatgaggaattaaggggcctccaattagtaaagataaatatatttattgtgcacttgatttatcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCACTCTACCGAGCTTGCACGAATTCTGAAG

Basic information

species Oryza sativa
transcript LOC_Os10g40030.11
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|29656761|gb|CB653036.1|CB653036
EST:     TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAG                         ATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
genomic: TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAGgtaattaata ... atcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
EST: gi|38471413|gb|CF955544.1|CF955544
EST:     TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAG                         ATTCTCCACTTATATTGCTTACG
genomic: TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAGgtaattaata ... atcttaccagATTCTCCACTTATATTGCTTACG
EST: gi|38477927|gb|CF962060.1|CF962060
EST:     TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAG                         ATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
genomic: TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAGgtaattaata ... atcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
EST: gi|3764142|gb|AU030642.1|AU030642
EST:     TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAG                         ATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
genomic: TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAGgtaattaata ... atcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
EST: gi|29656760|gb|CB653035.1|CB653035
EST:     TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAG                         ATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA
genomic: TTGACCTATCCTGAAGGGATATGTTTCGATAGTGTAAAAGATCTTTCGAGgtaattaata ... atcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctccaattagtaaagataaatatatttattgtgcacttgatttatcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCACTCTACCGAGCTTGCACGAATTCTGAAG
                                    acttgat  putative branch site (score: 5)
                                          tttatctt  CT-rich tract
      aattagtaaagataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactttagcttttgtcattctaatgttaacatgaggaattaaggggcctccaattagtaaagataaatatatttattgtgcacttgatttatcttaccagATTCTCCACTTATATTGCTTACGGCCAGTCCAAGCTTGCCAACATTTTGCACTCTACCGAGCTTGCACGAATTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG