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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTCTGAGGCAGAGGAAATAGATGTAGAGAGTCTTCTGGAATCACTAGAGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatctcttggatgtgctttctgcttggacttgaatctgcattatttggtccatgctatcttgcgacttaaagatccatggttacacaacagggg...

Basic information

species Oryza sativa
transcript LOC_Os08g45180.1
intron # 8
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|86499585|gb|CI142218.1|CI142218
EST:     ATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: ATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|86870825|gb|CI326656.1|CI326656
EST:     TGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATCTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: TGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|33823460|gb|CF337537.1|CF337537
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|88983214|gb|CI020778.1|CI020778
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|163927398|gb|EG710682.1|EG710682
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|29672290|gb|CB668565.1|CB668565
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|86905389|gb|CI285352.1|CI285352
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|86426902|gb|CI071999.1|CI071999
EST:     AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAG                         TCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
genomic: AGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA
EST: gi|86852922|gb|CI323231.1|CI323231
EST:     GCCAAAA-GCATCGCCTCCAAG                         TCAAA-TTGAGAATAAG-GCAGAT-GAATAGGATCCATCAGTGGCAGATTA
genomic: GCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTA

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), 72 (downstream exon)
Score: 17

TGCTTCTGAGGCAGAGGAAATAGATGTAGAGAGTCTTCTGGAATCACTAGAGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatc ... attgttttagTCAAATTTGAGAATAAGTGCAGATGGAATAGGATCCATCAGTGGCAGATTACTTTTAGGCACTGCCGAAATTATACCCTCTGAAGAGCTCATAGATACAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTCTGAGGCAGAGGAAATAGATGTAGAGAGTCTTCTGGAATCACTAGAGAAGAAAGAAGTTTTGAGTTCAAGCATGCCAAAATGCATCGCCTCCAAGgtatggcatctcttggatgtgctttctgcttggacttgaatctgcattatttggtccatgctatcttgcgacttaaagatccatggttacacaacagggg

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT