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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaacgttaggttgtttttttaagaaaaaaacactgttttatcggttattttttgcagcagtatctaattgttaacttggctactcttttgcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCATCGGTTTTTGGCAATGAAAGTGACGAAGAATCATGATCTTTGCCCGCCC

Basic information

species Oryza sativa
transcript LOC_Os04g02500.2
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|88251307|gb|CI349735.1|CI349735
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|29639865|gb|CB644874.1|CB644874
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|16579036|gb|BI813131.1|BI813131
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCC-AAATGGCTCCTTCCAAG                         GCTCCAGTT-GC-ATGTAAGCAAGAAACCTAAGGTTGCTAC-AAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|32947961|gb|BP184533.1|BP184533
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|29638463|gb|CB643472.1|CB643472
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|86492603|gb|CI135236.1|CI135236
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|87026150|gb|CI256893.1|CI256893
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|58694097|gb|CK082784.1|CK082784
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCGAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
EST: gi|86858897|gb|CI275113.1|CI275113
EST:     ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAG                         GCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA
genomic: ATCAGCGTAAAACCTTGAAGTTTGGCTTCTCCAAAATGGCTCCTTCCAAGgtaccccaca ... gcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttttgcagcagtatctaattgttaacttggctactcttttgcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCATCGGTTTTTGGCAATGAAAGTGACGAAGAATCATGATCTTTGCCCGCCC
                        tgttaac  putative branch site (score: 2)
                                      ctcttttgc  putative PPT
                tatctaattgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaacgttaggttgtttttttaagaaaaaaacactgttttatcggttattttttgcagcagtatctaattgttaacttggctactcttttgcacggacagGCTCCAGTTGGCAATGTAAGCAAGAAACCTAAGGTTGCTACAAAAATGTCATCGGTTTTTGGCAATGAAAGTGACGAAGAATCATGATCTTTGCCCGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - gttgttt
- - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagca