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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaaacacaataaatcattatgtaattcatgttatgttcattttgtggtaatttacactaaaactaattttgttctctttgtatattgctttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGGTCAGCATAGCTGCCCCCTTGGACATTAATCCTGTTTATGAAGGCCTGCA

Basic information

species Oryza sativa
transcript LOC_Os11g38610.2
intron # 10
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|86437252|gb|CI118974.1|CI118974
EST:     TACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTG                         CTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
genomic: TACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTGgtaatgttgc ... tttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
EST: gi|87014789|gb|CI269496.1|CI269496
EST:     TAATACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTG                         CTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
genomic: TAATACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTGgtaatgttgc ... tttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
EST: gi|27548886|gb|CA767041.2|CA767041
EST:     TAATACTGAGAGTAATGCTCCCAATCATCCGNCACGTTACTTCACAACTG                         CTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
genomic: TAATACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTGgtaatgttgc ... tttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
EST: gi|86480401|gb|CI123034.1|CI123034
EST:     TAATACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTG                         CTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG
genomic: TAATACTGAGAGTAATGCTCACAATCATCCGCCATGTTACTTCACAACTGgtaatgttgc ... tttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtaatttacactaaaactaattttgttctctttgtatattgctttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGGTCAGCATAGCTGCCCCCTTGGACATTAATCCTGTTTATGAAGGCCTGCA
                 aactaat  putative branch site (score: 2)
                                         ttgcttt  putative PPT
     aatttacactaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaaacacaataaatcattatgtaattcatgttatgttcattttgtggtaatttacactaaaactaattttgttctctttgtatattgctttgtcacagCTTTTGGCTATCCAAGTGAGAATGATAGCCATCTTGTCTCTGGATTACTGGTCAGCATAGCTGCCCCCTTGGACATTAATCCTGTTTATGAAGGCCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - caataaa
- - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa