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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACACAGAAGGAACCTCAAAGGCTGAGGAACCTGCCACTGGGAGCAAAGGGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatccattctgcattgtttgctattctgtattttatgtaatactttgaaaggctttcagtatcttggatgcatgcctttctgggttgaggccaagctttctttttgggtttgtgtggcatatacattcaggatcacagctaactcgaaacttgctcttgttag

Basic information

species Oryza sativa
transcript LOC_Os02g48010.1
intron # 8
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|29644320|gb|CB649327.1|CB649327
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|29672013|gb|CB668288.1|CB668288
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|89186494|gb|CI048166.1|CI048166
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|89181332|gb|CI112838.1|CI112838
EST:     CCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: CCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|88970588|gb|CI385278.1|CI385278
EST:     ACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: ACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|29658107|gb|CB654382.1|CB654382
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|88840733|gb|CI080187.1|CI080187
EST:     CAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: CAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|88994188|gb|CI116152.1|CI116152
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         TCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86260138|gb|CI066011.1|CI066011
EST:     GCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|163918541|gb|EG714351.1|EG714351
EST:     GCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86527190|gb|CI167396.1|CI167396
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86527171|gb|CI167377.1|CI167377
EST:     CCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: CCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|88588258|gb|CI706064.1|CI706064
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCCGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|88837598|gb|CI078958.1|CI078958
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|29638045|gb|CB643054.1|CB643054
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|87015180|gb|CI273578.1|CI273578
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|32947807|gb|BP184379.1|BP184379
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|29623423|gb|CB628434.1|CB628434
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|87015133|gb|CI273531.1|CI273531
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|3766585|gb|AU030695.1|AU030695
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86499146|gb|CI141779.1|CI141779
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|15855040|gb|BI807852.1|BI807852
EST:     TCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACAACACATGGCCCTGTAGAGGTCACTAGTGCCAGAGG
genomic: TCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGAC-ACACATGGCCCTGTAGAGGTCACTAGTG-CAGAGG
EST: gi|4714902|gb|AU056019.1|AU056019
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTNGTNCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|58668134|gb|CK056820.1|CK056820
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86435224|gb|CI106457.1|CI106457
EST:     TGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: TGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86488042|gb|CI130675.1|CI130675
EST:     CATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: CATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|29661394|gb|CB657669.1|CB657669
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
EST: gi|86481149|gb|CI123782.1|CI123782
EST:     GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAG                         GCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG
genomic: GGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGG

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: 69 (upstream exon), 8 (downstream exon)
Score: 3

TGACACAGAAGGAACCTCAAAGGCTGAGGAACCTGCCACTGGGAGCAAAGGGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatcca ... ctcttgttagGCTGAAGCTGGTGACACACATGGCCCTGTAGAGGTCACTAGTGCAGAGGGGGTAGATATTGTGGATGGTATAGATGCAGCACCAGATGCGATGCCTATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACACAGAAGGAACCTCAAAGGCTGAGGAACCTGCCACTGGGAGCAAAGGGGCCTCCCAATCAGCTGATGATGCATCTCAATTACCCGAGTACTCGCAGgtaagatccattctgcattgtttgctattctgtattttatgtaatactttgaaaggctttcagtatcttggatgcatgcctttctgggttgaggccaagctttctttttgggtttgtgtggcatatacattcaggatcacagctaactcgaaacttgctcttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT