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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgcatgcatgccttatattatggaacaactttaaaaagtagttgtgccttatattatgaaatggagggagttaatgaaaacatcatctgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCTGACTTGGTTGAGAAAGTTAATGGGTTACTTGATGAGGTTCAGAAAAACT

Basic information

species Oryza sativa
transcript LOC_Os12g25710.3
intron # 9
splice site 3'
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|29665238|gb|CB661513.1|CB661513
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29612729|gb|CB617742.1|CB617742
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|218493888|gb|FG946861.1|FG946861
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29616050|gb|CB621062.1|CB621062
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29622778|gb|CB627789.1|CB627789
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT

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: 75 (upstream exon), 75 (downstream exon)
Score: 74

CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCTGACTTGGTTGAGAAAGTTAATGGGTTACTTGATGAGGTTCAGAAAAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgccttatattatgaaatggagggagttaatgaaaacatcatctgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCTGACTTGGTTGAGAAAGTTAATGGGTTACTTGATGAGGTTCAGAAAAACT
                          agttaat  putative branch site (score: 74)
                                           tctgcttttc  putative PPT
      ttatattatgaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcatgcatgccttatattatggaacaactttaaaaagtagttgtgccttatattatgaaatggagggagttaatgaaaacatcatctgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCTGACTTGGTTGAGAAAGTTAATGGGTTACTTGATGAGGTTCAGAAAAACT

gcatgca
- -tgcatgc
- - - - - - - - - - - - -gaacaac
- - - - - - - - - - - - - - - - - -aaaaagta
- - - - - - - - - - - - - - - - - - - - - - - gtgcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatca