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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatcagctattaataattcttagggctccctgtcggaagtccaaattcttatccactcttgtgtttcctatgctgatcttgtcgtatcacaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAAAAGGGACAGAGTTGTGGAGTTTCAGACCAAGCTTGCCACAGCAAAAGCA

Basic information

species Oryza sativa
transcript LOC_Os07g06980.1
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|88427334|gb|CI569372.1|CI569372
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88587229|gb|CI704965.1|CI704965
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88720048|gb|CI745138.1|CI745138
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88390145|gb|CI605598.1|CI605598
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAAAAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88468894|gb|CI696900.1|CI696900
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88590701|gb|CI707582.1|CI707582
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88301198|gb|CI594724.1|CI594724
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88718451|gb|CI741961.1|CI741961
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88693576|gb|CI737151.1|CI737151
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGNATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|86850055|gb|CI303508.1|CI303508
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88404447|gb|CI578324.1|CI578324
EST:     GCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCT-CAG                         ATTGGGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTAAACAGCCAA
genomic: GCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|29681279|gb|CB677554.1|CB677554
EST:     GCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: GCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88336860|gb|CI626940.1|CI626940
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88587525|gb|CI705279.1|CI705279
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88432409|gb|CI565442.1|CI565442
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88367852|gb|CI570591.1|CI570591
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88721491|gb|CI744790.1|CI744790
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|117232793|gb|CT842287.1|CT842287
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88417010|gb|CI573725.1|CI573725
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88590249|gb|CI709087.1|CI709087
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88316146|gb|CI620424.1|CI620424
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|29644493|gb|CB649500.1|CB649500
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88312349|gb|CI582687.1|CI582687
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88432973|gb|CI690831.1|CI690831
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88577273|gb|CI673839.1|CI673839
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
EST: gi|88440911|gb|CI693488.1|CI693488
EST:     AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAG                         ATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA
genomic: AAATCCAATCGCGAGAGGCGAGCGCCGCCGCCGCCGGGATCGCCCTCCAGgtacggccgc ... acaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttatccactcttgtgtttcctatgctgatcttgtcgtatcacaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAAAAGGGACAGAGTTGTGGAGTTTCAGACCAAGCTTGCCACAGCAAAAGCA
                           tgctgat  putative branch site (score: 3)
                                             acaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatcagctattaataattcttagggctccctgtcggaagtccaaattcttatccactcttgtgtttcctatgctgatcttgtcgtatcacaattacagATTGCGTTGCATGCTCTGATGGCGTCTGATATGAGGTCACTCAACAGCCAAAAGGGACAGAGTTGTGGAGTTTCAGACCAAGCTTGCCACAGCAAAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT