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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCTCCCCTCATCTCCGCCGGTCGCCTCCTCCAAGCCTCCGCGACGCGCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcaccctcccatcccgatccttcccgctgcaaaaccccccatccgattcgcccgacgcggggggcgttccgtgtaggaattgatggtgattgtgg...

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 1
splice site 5'
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|88396304|gb|CI598416.1|CI598416
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88426420|gb|CI576662.1|CI576662
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|33684443|gb|CF312682.1|CF312682
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88370337|gb|CI587727.1|CI587727
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|117222072|gb|CT852607.1|CT852607
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACCTGCGCTCTCTCAAG                         AGATACAGTTCTAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88411046|gb|CI606265.1|CI606265
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88738586|gb|CI762094.1|CI762094
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88364211|gb|CI612160.1|CI612160
EST:     GCACGGAAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88392412|gb|CI612886.1|CI612886
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88359996|gb|CI608510.1|CI608510
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|33681307|gb|CF309546.1|CF309546
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88364616|gb|CI612431.1|CI612431
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88430305|gb|CI567324.1|CI567324
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88316412|gb|CI621651.1|CI621651
EST:     GCACGGGAGAGATGTACCGCATCGCCGGGAGCCAATTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88402213|gb|CI615056.1|CI615056
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|163919795|gb|EG711485.1|EG711485
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|163922995|gb|EG712768.1|EG712768
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|58587739|gb|CF986047.1|CF986047
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACCTGCGCTCTCTCAAG                         AGATACAGTTCTAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88294602|gb|CI602322.1|CI602322
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88402185|gb|CI615028.1|CI615028
EST:     GCACGGCAGAGATTTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88364158|gb|CI610502.1|CI610502
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATAAAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88401660|gb|CI588601.1|CI588601
EST:     GCACGGAAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTAAAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|33810480|gb|CF331128.1|CF331128
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|88398886|gb|CI601222.1|CI601222
EST:     GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
EST: gi|40490205|gb|BX899810.1|BX899810
EST:     GCCGGGAGCCACTTGCGCTCTCTCAAG                         AGATACAGTTATAGTATGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA
genomic: GCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 52 (upstream exon), 72 (downstream exon)
Score: 43

GGCGGCTCCCCTCATCTCCGCCGGTCGCCTCCTCCAAGCCTCCGCGACGCGCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcacc ... gtggttgcagAGATACAGTTATAGTAGGTTTGCTAGTACAAGTGTTGTGAAGCAGTCTTCAGGTGGTTTGTTTAGCTGGCTTCTTGGGGAGAAGTCAAGCCAATTGCCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGCTCCCCTCATCTCCGCCGGTCGCCTCCTCCAAGCCTCCGCGACGCGCACGGCAGAGATGTACCGCATCGCCGGGAGCCACTTGCGCTCTCTCAAGgtaccgcaccctcccatcccgatccttcccgctgcaaaaccccccatccgattcgcccgacgcggggggcgttccgtgtaggaattgatggtgattgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggcg