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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagggttcatgcgttttattctttatattatatggaccatgtaggaatgcaatttctttcaaatctaagaagttatttcaatttttttgcaatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGATAATGAACTTAGTTAGAAATTCAAAGCTCGATGCCAAGATTGATTCAGTG

Basic information

species Oryza sativa
transcript LOC_Os07g07250.1
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|4716113|gb|AU057229.1|AU057229
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|58689367|gb|CK078054.1|CK078054
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|29616632|gb|CB621644.1|CB621644
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CCTGCTCTCTCAGAAACTGAACATGCGCTATGATG
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATG
EST: gi|86430950|gb|CI083373.1|CI083373
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTTATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|44675035|gb|CR288469.1|CR288469
EST:     CCATTGATATCGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGACTTGTGGAT
genomic: CCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|29616633|gb|CB621645.1|CB621645
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CCTGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|113931019|gb|DQ884113.1|DQ884113
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTTATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|86414045|gb|CI068252.1|CI068252
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|29660023|gb|CB656298.1|CB656298
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|88263159|gb|CI366933.1|CI366933
EST:     AACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAGGGGGAGTTGTGGAT
genomic: AACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|58676883|gb|CK065570.1|CK065570
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
EST: gi|58684643|gb|CK073330.1|CK073330
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGG                         CATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGAT

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: 74 (upstream exon), 75 (downstream exon)
Score: 28

GGAATTCCATCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTCCATTGATATTGGgtgggtgttt ... caatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGATAATGAACTTAGTTAGAAATTCAAAGCTCGATGCCAAGATTGATTCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgcaatttctttcaaatctaagaagttatttcaatttttttgcaatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGATAATGAACTTAGTTAGAAATTCAAAGCTCGATGCCAAGATTGATTCAGTG
                                     tttttttgc  CT-rich tract
                aaatctaagaagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagggttcatgcgttttattctttatattatatggaccatgtaggaatgcaatttctttcaaatctaagaagttatttcaatttttttgcaatgaacagCATGCTCTCTCAGAAACTGAACATGCGCTATGATGAAGGGGAGTTGTGGATAATGAACTTAGTTAGAAATTCAAAGCTCGATGCCAAGATTGATTCAGTG

- - - ttcatgc
- - - - - - - - - - - - - - - - - - -ccatgta
- - - - - - - - - - - - - - - - - - - - - - -gaatgca