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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatcacctacttcttttcatgcttggaagtttgtagcctgtagtatgtaaattttacgccctacttagttcaggcactatgaatgcaagagatttacgccctactgatcgattaaatcgcatatgaattgcgcccttatgttcagacggctgatgtgcgcacctgtcactaaaacag

Basic information

species Oryza sativa
transcript LOC_Os06g28060.2
intron # 20
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|29642488|gb|CB647495.1|CB647495
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86437224|gb|CI118946.1|CI118946
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|66920553|gb|CX107401.1|CX107401
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86437904|gb|CI119824.1|CI119824
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|29687744|gb|CB684019.1|CB684019
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86892642|gb|CI312037.1|CI312037
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86597685|gb|CI274676.1|CI274676
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86479104|gb|CI121737.1|CI121737
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|38474302|gb|CF958434.1|CF958434
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|58665464|gb|CK054150.1|CK054150
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86482331|gb|CI124964.1|CI124964
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|23513633|gb|BU673231.1|BU673231
EST:     TCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: TCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|30227501|gb|CB965393.1|CB965393
EST:     ACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: ACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|88520687|gb|CI448341.1|CI448341
EST:     AACTCTTATGTAAG                         GCAGACCCCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: AACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|86596961|gb|CI270757.1|CI270757
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|88477557|gb|CI414828.1|CI414828
EST:     TGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: TGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|14981332|gb|BI306010.1|BI306010
EST:     GCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|29626226|gb|CB631237.1|CB631237
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|88472952|gb|CI410223.1|CI410223
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|29687745|gb|CB684020.1|CB684020
EST:     GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAG                         GCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|23513647|gb|BU673238.1|BU673238
EST:     ACTCTTATGTAAG                         GCAGA-CGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
genomic: ACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|88284594|gb|CI406040.1|CI406040
EST:     AGGCATCAGAGCACCAACTCTTATGTAAG                         GCAGACCGGTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAN
genomic: AGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG
EST: gi|88543924|gb|CI473978.1|CI473978
EST:     CTCTTATGTAAG                         GCAGACCGCTTACGAGACGAGCTCCTTGANTGGCATGAGATGTACAAGAAG
genomic: CTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAG

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: 57 (upstream exon), 19 (downstream exon)
Score: 1

GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatca ... actaaaacagGCAGACCGCTTACGAAACGAGCTCCTTGAGTGGCATGAGATGTACAAGAAGCTAACCGACGAGGTGAAATTCTACGATGGCCTATACGCATTGCAGCGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTCTAAACTTGAGGCATCAGAGCAGCAACTCTTATGTAAGgtatgtatcacctacttcttttcatgcttggaagtttgtagcctgtagtatgtaaattttacgccctacttagttcaggcactatgaatgcaagagatttacgccctactgatcgattaaatcgcatatgaattgcgcccttatgttcagacggctgatgtgcgcacctgtcactaaaacag

- - - - - - - - - -  AGAGCA
- - - - - - - - - - - GAGCAG