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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtcctatgccaaatgtgcctatagtgtgtttcacacttattgatcactaattcactatccatttttcttttactaaacatggtttatcgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATGTGATGATTGCCTACCAAATGGCAATGAAGTGGGCAACTTATTAGATATA

Basic information

species Oryza sativa
transcript LOC_Os11g06130.2
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|88332302|gb|CI656171.1|CI656171
EST:     TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATG                         ATACTGTTTTGATCCAGTTATTTATGATGGATCATTACTAGAGTGGTTATG
genomic: TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATGgtacggcttt ... cgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATG
EST: gi|88692242|gb|CI735817.1|CI735817
EST:     TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATG                         ATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTAT
genomic: TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATGgtacggcttt ... cgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTAT
EST: gi|88329411|gb|CI648466.1|CI648466
EST:     TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATG                         ATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATG
genomic: TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATGgtacggcttt ... cgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATG
EST: gi|88340596|gb|CI647550.1|CI647550
EST:     TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATG                         ATACTGTTTTGATC
genomic: TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATGgtacggcttt ... cgttttgtagATACTGTTTTGATC
EST: gi|88693268|gb|CI736843.1|CI736843
EST:     TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATG                         ATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATG
genomic: TTCCGGGGCTTGATGCGTGAGAGGAGCTTCTGAAGTCGCAGGAAAAAATGgtacggcttt ... cgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactaattcactatccatttttcttttactaaacatggtttatcgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATGTGATGATTGCCTACCAAATGGCAATGAAGTGGGCAACTTATTAGATATA
                            tactaaa  putative branch site (score: 1)
                                            tcgtttt  putative PPT
                  atttttcttttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtcctatgccaaatgtgcctatagtgtgtttcacacttattgatcactaattcactatccatttttcttttactaaacatggtttatcgttttgtagATACTGTTTTGATCCAGTTATTTATGATGGATCATTAGTAGAGTGGTTATGTGATGATTGCCTACCAAATGGCAATGAAGTGGGCAACTTATTAGATATA

- - - ctatgcc
- - - - - - - - -gtgccta
- - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggtt