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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgtcccacttatctgatctcacttgactattgtctgacagcctcacaaaagaaaagaaatttttctgacattttttttttgaaaaatgcattattttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCCTTGTTCAAGGCTGTTGCACCAGCTGGCGCAGGTGTTCT

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 14
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|86431076|gb|CI083499.1|CI083499
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|88841567|gb|CI080823.1|CI080823
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|29678071|gb|CB674346.1|CB674346
EST:     ATAACTATAATTACGGGCACTTCTTTTTTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|86260630|gb|CI066503.1|CI066503
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|86494925|gb|CI137558.1|CI137558
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|29680055|gb|CB676330.1|CB676330
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|86870704|gb|CI323580.1|CI323580
EST:     CTCTTCTACAAAACAAAGCAGTT                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: CTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|89186840|gb|CI052253.1|CI052253
EST:     AACTATAATTACGGGCACTTCTCTTCTACCAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: AACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|88842694|gb|CI081950.1|CI081950
EST:     AAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: AAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|87006928|gb|CI275236.1|CI275236
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|29644402|gb|CB649409.1|CB649409
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|87025643|gb|CI250137.1|CI250137
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|29679866|gb|CB676141.1|CB676141
EST:     ATAACTATAATTACGGGCACTTCTCTTTTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|88841121|gb|CI080575.1|CI080575
EST:     ATAACTATAATTACGGGCACTTCCCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
EST: gi|89193059|gb|CI050357.1|CI050357
EST:     ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG                         CCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC
genomic: ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCC

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: 61 (upstream exon), 61 (downstream exon)
Score: 9

ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTGgtacttgtcc ... attttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCCTTGTTCAAGGCTGTTGCACCAGCTGGCGCAGGTGTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaaaagaaatttttctgacattttttttttgaaaaatgcattattttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCCTTGTTCAAGGCTGTTGCACCAGCTGGCGCAGGTGTTCT
               ttctgac  putative branch site (score: 9)
                                           ttatttt  putative PPT
     aaagaaatttttctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgtcccacttatctgatctcacttgactattgtctgacagcctcacaaaagaaaagaaatttttctgacattttttttttgaaaaatgcattattttgacagCCACAAGGGCAACGGGGTGCTGCAAACGGAATAGCTACAACGGCCATGTCCTTGTTCAAGGCTGTTGCACCAGCTGGCGCAGGTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG