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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTTGATGGTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgacaattgccgccgctgtcatttattttatggacttaccaattctcactcatgtatttctttaatgtaatgatggtttagtgtgtctctattactcactcattcagcaattatattgttgaaaactacttgaccgaaggtggtatatttaatttctcaccttcacttgtatccgcgcag

Basic information

species Oryza sativa
transcript LOC_Os10g40780.3
intron # 44
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|12405034|gb|AU166635.1|AU166635
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|9886370|gb|BE607462.1|BE607462
EST:     GCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|428676|gb|D24828.1|D24828
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|58681156|gb|CK069843.1|CK069843
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|428473|gb|D24623.1|D24623
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAAGCAGGAGTTACTTCTGCC
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAA-GCAGAAGTTACTTCTGCC
EST: gi|29674319|gb|CB670594.1|CB670594
EST:     TTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACTTCAAG                         AGGCCAGATGGATCCTTTTTAACTGA-TTAAAGCAGAAGTTACTTCTGCCG
genomic: TTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|163928760|gb|EG711897.1|EG711897
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAG
EST: gi|428499|gb|D24650.1|D24650
EST:     GTGCCTTAAAGTCAAAGCAAATGNAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGANGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|58677103|gb|CK065790.1|CK065790
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
EST: gi|428675|gb|D24827.1|D24827
EST:     GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAG                         AGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG
genomic: GTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCG

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: 71 (upstream exon), 71 (downstream exon)
Score: 13

TCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTTGATGGTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgaca ... atccgcgcagAGGCCAGATGGATCCTTTTTAACTGATTTAAAGCAGAAGTTACTTCTGCCGCAAAACGAAGCAAATATTGCTGGGACTCGTTACAATGTACCTCTTGTTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTTGATGGTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACCTCAAGgtgaatgacaattgccgccgctgtcatttattttatggacttaccaattctcactcatgtatttctttaatgtaatgatggtttagtgtgtctctattactcactcattcagcaattatattgttgaaaactacttgaccgaaggtggtatatttaatttctcaccttcacttgtatccgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA