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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCCGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgttgccgcgcttctctttttcatcgtttcaagcctgagatcccttttgttagaaatgtatgaacgtgttattaatgttaacgatttttagtga...

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 2
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|4715628|gb|AU056744.1|AU056744
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33658304|gb|CF280918.1|CF280918
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33658126|gb|CF280740.1|CF280740
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33690612|gb|CF318851.1|CF318851
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|14714076|gb|AU198016.1|AU198016
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88312635|gb|CI587543.1|CI587543
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33679537|gb|CF307776.1|CF307776
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88316617|gb|CI622863.1|CI622863
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|58664366|gb|CK053052.1|CK053052
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|58677950|gb|CK066637.1|CK066637
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCGGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88332593|gb|CI651753.1|CI651753
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33822526|gb|CF337070.1|CF337070
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|86906721|gb|CI291169.1|CI291169
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|33658022|gb|CF280636.1|CF280636
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|58598104|gb|CK008632.1|CK008632
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88728556|gb|CI752066.1|CI752066
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88445308|gb|CI587202.1|CI587202
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|88696206|gb|CI739781.1|CI739781
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|2428191|gb|C72654.1|C72654
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
EST: gi|58694105|gb|CK082792.1|CK082792
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGG                         ATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCC

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: 74 (upstream exon), 74 (downstream exon)
Score: 60

CCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCCGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgtt ... tactctccagATTCTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCCGAAGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCCGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAAGAACTACGGgtaacttgttgccgcgcttctctttttcatcgtttcaagcctgagatcccttttgttagaaatgtatgaacgtgttattaatgttaacgatttttagtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC