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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGTGGGCGGGCTCTCTCCCTCTTCCTCCTCCGCTCCGCTCCACCTCGGTTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatccatccatccatccacgctgctgctcggctcttgtaggtttttgattcccctcgtttgggtacgctcttgctgtggttcctgctgtttgtt...

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
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|58666860|gb|CK055546.1|CK055546
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58674399|gb|CK063085.1|CK063085
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88316515|gb|CI622761.1|CI622761
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58604235|gb|CK014763.1|CK014763
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|29627233|gb|CB632244.1|CB632244
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         GGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88436650|gb|CI691382.1|CI691382
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58659927|gb|CK048607.1|CK048607
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88451891|gb|CI694666.1|CI694666
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|117237395|gb|CT861888.1|CT861888
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58670476|gb|CK059162.1|CK059162
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|33678911|gb|CF307150.1|CF307150
EST:     GGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: GGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88593233|gb|CI709394.1|CI709394
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58678394|gb|CK067081.1|CK067081
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58605908|gb|CK033941.1|CK033941
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCAGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58675377|gb|CK064064.1|CK064064
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58672618|gb|CK061304.1|CK061304
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|38471514|gb|CF955645.1|CF955645
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88391925|gb|CI683743.1|CI683743
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58664329|gb|CK053015.1|CK053015
EST:     GACCACCACCCGATCGGCGGCGAGGTGCGGGGAGCTCCGTGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: GACCACCACCCGATCGGCGGCGAGG-GCGGGGAGCTCCG-GCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58671476|gb|CK060162.1|CK060162
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|29616519|gb|CB621531.1|CB621531
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCAGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58668341|gb|CK057027.1|CK057027
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58680986|gb|CK069673.1|CK069673
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|29672730|gb|CB669005.1|CB669005
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58598230|gb|CK008758.1|CK008758
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58690725|gb|CK079412.1|CK079412
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|33797130|gb|CF324430.1|CF324430
EST:     GCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: GCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58669222|gb|CK057908.1|CK057908
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|58658129|gb|CK046809.1|CK046809
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGGGGTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
EST: gi|88321968|gb|CI673117.1|CI673117
EST:     TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAG                         TGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA
genomic: TTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGA

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: 68 (upstream exon), 75 (downstream exon)
Score: 67

CCAGTGGGCGGGCTCTCTCCCTCTTCCTCCTCCGCTCCGCTCCACCTCGGTTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatc ... atattaccagTGAAAATGGATGGAAATGCTAAAGGCGGTGGGCATTCTGAGGCACTGAAGAACTACAATCTTGGAAGAACTTTAGGTATTGGCTCATTTGGAAAAGTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGTGGGCGGGCTCTCTCCCTCTTCCTCCTCCGCTCCGCTCCACCTCGGTTGACCACCACCCGATCGGCGGCGAGGGCGGGGAGCTCCGGCGTGCTCAGgtaatccatccatccatccatccacgctgctgctcggctcttgtaggtttttgattcccctcgtttgggtacgctcttgctgtggttcctgctgtttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcg