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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaggtaccaaattttacactagaaaatgtggtatttcccggtactttttcaaggatgataaaattacccttacatgatactccatatttctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGGTAGCGGATCGTATTGGCCGAAAGCCTGTCATTATCTTTTCCATTTTTGC

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 3
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|29680054|gb|CB676329.1|CB676329
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|29674310|gb|CB670585.1|CB670585
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|29644401|gb|CB649408.1|CB649408
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|33677870|gb|CF306109.1|CF306109
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88334950|gb|CI648725.1|CI648725
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88330064|gb|CI652455.1|CI652455
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|33677492|gb|CF305731.1|CF305731
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88347612|gb|CI634297.1|CI634297
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|29682083|gb|CB678358.1|CB678358
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|29679865|gb|CB676140.1|CB676140
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88332574|gb|CI651734.1|CI651734
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88353644|gb|CI633035.1|CI633035
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|33678908|gb|CF307147.1|CF307147
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|29678070|gb|CB674345.1|CB674345
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
EST: gi|88303400|gb|CI669048.1|CI669048
EST:     GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG                         GCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG
genomic: GCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTGgtattaacat ... tctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttcaaggatgataaaattacccttacatgatactccatatttctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGGTAGCGGATCGTATTGGCCGAAAGCCTGTCATTATCTTTTCCATTTTTGC
                       cccttac  putative branch site (score: 3)
                                           tttctgct  putative PPT
           atgataaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaggtaccaaattttacactagaaaatgtggtatttcccggtactttttcaaggatgataaaattacccttacatgatactccatatttctgctgcagGCGCATCATATATGATCGGTCGAGGTTTTGCATCAATCTTGTGGGGTATGGTAGCGGATCGTATTGGCCGAAAGCCTGTCATTATCTTTTCCATTTTTGC

- - - -accaaat
- - - - - - - - - - ctagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccata