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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaaacatccttcattcttttctctgttatttccatatcattcttctacactgaaagtggtcatatcatcaattatcttttgaatgcattttttttcctgatattacctcctcctcgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGAGGAGGATGACATGTTCAAATGATATTAATTGTGAGAAAGCTTCCAGGGA

Basic information

species Oryza sativa
transcript LOC_Os09g36220.2
intron # 5
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|58605432|gb|CK033465.1|CK033465
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|33676452|gb|CF304691.1|CF304691
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTC
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTC
EST: gi|29670836|gb|CB667111.1|CB667111
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTANAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|58691786|gb|CK080473.1|CK080473
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|218483797|gb|FG943383.1|FG943383
EST:     ACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: ACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29645661|gb|CB650668.1|CB650668
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29638275|gb|CB643284.1|CB643284
EST:     CAAGCCTGACCACAAGAACACCGACAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|33798193|gb|CF324956.1|CF324956
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|58693630|gb|CK082317.1|CK082317
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29679591|gb|CB675866.1|CB675866
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29679636|gb|CB675911.1|CB675911
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|58694414|gb|CK083101.1|CK083101
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|33675681|gb|CF303920.1|CF303920
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAG
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAG
EST: gi|58695431|gb|CK084118.1|CK084118
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29687696|gb|CB683971.1|CB683971
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|29625624|gb|CB630635.1|CB630635
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACCGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|157650088|gb|EX449722.1|EX449722
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
EST: gi|66915487|gb|CX102335.1|CX102335
EST:     CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATG                         CATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA
genomic: CAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGA

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: 73 (upstream exon), 71 (downstream exon)
Score: 47

CAAACCAACAATTTACTGGAATATAAGCAGCCAATGGGAAGGCATTTCTCCAAGCCTGACCACAAGAACACCGAGAAAAATGGAGGGACTAAAATTCATGgtaataaaac ... cgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGAGGAGGATGACATGTTCAAATGATATTAATTGTGAGAAAGCTTCCAGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatcttttgaatgcattttttttcctgatattacctcctcctcgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGAGGAGGATGACATGTTCAAATGATATTAATTGTGAGAAAGCTTCCAGGGA
                         tcctgat  putative branch site (score: 47)
                  ttttttttcctgatat  CT-rich tract
            aatgcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaaacatccttcattcttttctctgttatttccatatcattcttctacactgaaagtggtcatatcatcaattatcttttgaatgcattttttttcctgatattacctcctcctcgttttgcagCATCTAATGATGGCAACTTGATTCCACGGAGGGAAGAGGATGCATCACTGAGGAGGATGACATGTTCAAATGATATTAATTGTGAGAAAGCTTCCAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG