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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaagatttatcagtggaaccatggctgattggctggtagacagtgtgaacttgaacgttgatatgataatgactctgttggtagtaatccatg...

Basic information

species Oryza sativa
transcript LOC_Os01g60410.3
intron # 2
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|88588887|gb|CI706732.1|CI706732
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58593001|gb|CF991309.1|CF991309
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|163917796|gb|EG712134.1|EG712134
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|1631641|gb|C19370.1|C19370
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58690981|gb|CK079668.1|CK079668
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58677585|gb|CK066272.1|CK066272
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58683175|gb|CK071862.1|CK071862
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGG--ATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58592288|gb|CF990596.1|CF990596
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58600789|gb|CK011317.1|CK011317
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGAGCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|163925769|gb|EG714605.1|EG714605
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|88391945|gb|CI683764.1|CI683764
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58594364|gb|CF992672.1|CF992672
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58684372|gb|CK073059.1|CK073059
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58592931|gb|CF991239.1|CF991239
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|33688145|gb|CF316384.1|CF316384
EST:     TCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: TCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|38470328|gb|CF954459.1|CF954459
EST:     CAAGGAACTAAAGGACCTGGAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|218501187|gb|FG953295.1|FG953295
EST:     AGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: AGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58600178|gb|CK010706.1|CK010706
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|58683224|gb|CK071911.1|CK071911
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|112785779|gb|EE591396.1|EE591396
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|87006558|gb|CI294941.1|CI294941
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|33688146|gb|CF316385.1|CF316385
EST:     CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|33810778|gb|CF331283.1|CF331283
EST:     CATCATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: CATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
EST: gi|3107124|gb|D42862.1|D42862
EST:     ATGCAGTGCAG                         GTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC
genomic: ATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTC

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), 61 (downstream exon)
Score: 200

GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaa ... ataaatttagGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTCCAGATAGTCCCTATGCTGGTGGAGTTTTCTTAGTGAATATTCATTTCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAGgtatgagaaagatttatcagtggaaccatggctgattggctggtagacagtgtgaacttgaacgttgatatgataatgactctgttggtagtaatccatg

- - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - -  CTGCAG