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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattgagcttatcactttgcatcttgcaccatgtttttcaaccaacagtagtgaatccaacgtaaatcatagttcagatggttgcaatatattgctcttgatcctcctctttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g14950.1
intron # 11
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|88305966|gb|CI634963.1|CI634963
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88490827|gb|CI428099.1|CI428099
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88333965|gb|CI645379.1|CI645379
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88851519|gb|CI670959.1|CI670959
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88475569|gb|CI412840.1|CI412840
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88480706|gb|CI417977.1|CI417977
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88283818|gb|CI405264.1|CI405264
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCNTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88476916|gb|CI414187.1|CI414187
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88347292|gb|CI632577.1|CI632577
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88472140|gb|CI409411.1|CI409411
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|33799625|gb|CF325673.1|CF325673
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88331000|gb|CI638408.1|CI638408
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|29637025|gb|CB642034.1|CB642034
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|29642738|gb|CB647745.1|CB647745
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88334143|gb|CI641194.1|CI641194
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
EST: gi|88281252|gb|CI402450.1|CI402450
EST:     ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG                         GTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC
genomic: ATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCC

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: 49 (upstream exon), 28 (downstream exon)
Score: 2

CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattg ... ctctttgcagGTTGCACGAACTGGCAGGGTTGCGTTGCGCCGTGAGTCAGGAGTCGATTCCAAATACCTCCGTGGGTTTTCCCTTCCTCTGTAGTTTGTTTGTCAGTTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAGgtttgtattgagcttatcactttgcatcttgcaccatgtttttcaaccaacagtagtgaatccaacgtaaatcatagttcagatggttgcaatatattgctcttgatcctcctctttgcag

- - - - - - - - - - - - - - - - - - AGGATG