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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATACCGATTATTGCTGCTTATCCCTTTATGACGCACTTATCAGGAATAAGACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactttatgaacctatgatttatatttttaaaaaaaaataattctaaaagtataaactctcatatatattttttagtaaacctgttggctactcc...

Basic information

species Oryza sativa
transcript LOC_Os11g04030.4
intron # 7
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|86431076|gb|CI083499.1|CI083499
EST:     GCAATGATCAAAAGTGTTCATGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|88841567|gb|CI080823.1|CI080823
EST:     GTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|29678071|gb|CB674346.1|CB674346
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTTTTTTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|86260630|gb|CI066503.1|CI066503
EST:     ATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: ATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|86494925|gb|CI137558.1|CI137558
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|29680055|gb|CB676330.1|CB676330
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|87006928|gb|CI275236.1|CI275236
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|29644402|gb|CB649409.1|CB649409
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|87025643|gb|CI250137.1|CI250137
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|29679866|gb|CB676141.1|CB676141
EST:     GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTTTACAAAACAAAGCAGTG
genomic: GACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|88841121|gb|CI080575.1|CI080575
EST:     AGTGCAGCAATGATCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCCCTTCTACAAAACAAAGCAGTG
genomic: AGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
EST: gi|89193059|gb|CI050357.1|CI050357
EST:     TCAAAAGTGTTCTTGCT                         ATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG
genomic: TCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG

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: 53 (upstream exon), 73 (downstream exon)
Score: 8

TATACCGATTATTGCTGCTTATCCCTTTATGACGCACTTATCAGGAATAAGACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactt ... tgttgatcagATAACTATAATTACGGGCACTTCTCTTCTACAAAACAAAGCAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATACCGATTATTGCTGCTTATCCCTTTATGACGCACTTATCAGGAATAAGACTTGGTGTGGCCCTCTATAGTGCAGCAATGATCAAAAGTGTTCTTGCTgtaagtactttatgaacctatgatttatatttttaaaaaaaaataattctaaaagtataaactctcatatatattttttagtaaacctgttggctactcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa