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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtatcattccattttggatgaatttgcctgtgtgccactagaattaactgtaagacaaatatgcatgcttactgaagatgatctgtggtttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g50840.1
intron # 7
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|86514557|gb|CI157190.1|CI157190
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|87021834|gb|CI278001.1|CI278001
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|55410939|gb|CV723315.1|CV723315
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|86514593|gb|CI157226.1|CI157226
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|88961736|gb|CI096928.1|CI096928
EST:     TTGTTCACAGCCATGAGGATCTTGCCAAAAAACTNAAG                         GATGCAAGGGATATAAATAAGAAGTCATCTTCAG
genomic: TTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|88841090|gb|CI001052.1|CI001052
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|86253223|gb|CI058148.1|CI058148
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|86477980|gb|CI120613.1|CI120613
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCCAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|88849869|gb|CI001575.1|CI001575
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|87036096|gb|CI189543.1|CI189543
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|88228874|gb|CI226725.1|CI226725
EST:     TGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: TGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|29616638|gb|CB621650.1|CB621650
EST:     CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|89186097|gb|CI047966.1|CI047966
EST:     CCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
EST: gi|88844980|gb|CI022334.1|CI022334
EST:     CTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAG                         GATGCAATGGATATAAATAAGAAGTCATCTTCAG
genomic: CTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG

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), 34 (downstream exon)
Score: 27

GCTGAAGTTTCTCAAAGACTGAACAATGCAAGGGAAGCGGCAAATCGGCCTATTGTTCACAGCCATGAGGATCTTGCCAAAAAACTTAAGgtgcacactt ... tttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactgtaagacaaatatgcatgcttactgaagatgatctgtggtttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG
           acaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtatcattccattttggatgaatttgcctgtgtgccactagaattaactgtaagacaaatatgcatgcttactgaagatgatctgtggtttgatacagGATGCAATGGATATAAATAAGAAGTCATCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - cattcca
- - - - - - - -ttggatg
- - - - - - - - - - - - -ttgcctg
- - - - - - - - - - - - - - - - -gtgccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatctg