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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggagggacattttcagaggataatcagcacttcccactagcaacaaaaacaattaaacaatactcaatcatagaattgctatctttttttacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGACAATCCTCCACCACCTGGAGGAGATGTCATATTCACGGATGATGTGAGCT

Basic information

species Oryza sativa
transcript LOC_Os08g36994.1
intron # 13
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|87016525|gb|CI273735.1|CI273735
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88514868|gb|CI442522.1|CI442522
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|2797227|gb|AA750521.1|AA750521
EST:     AGCGGTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86885927|gb|CI319775.1|CI319775
EST:     GTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: GTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88839144|gb|CI378068.1|CI378068
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|9865041|gb|AU100791.1|AU100791
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|29622603|gb|CB627614.1|CB627614
EST:     AGCGGTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|89175029|gb|CI041107.1|CI041107
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88838779|gb|CI376317.1|CI376317
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86494160|gb|CI136793.1|CI136793
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|58693961|gb|CK082648.1|CK082648
EST:     AGCGGTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86885390|gb|CI318541.1|CI318541
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATAT-GTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86477675|gb|CI120308.1|CI120308
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86599187|gb|CI355804.1|CI355804
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88970221|gb|CI383723.1|CI383723
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86437940|gb|CI119860.1|CI119860
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86888989|gb|CI314605.1|CI314605
EST:     AGCGCTTTCCTGTTCCTCTTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|89186541|gb|CI048213.1|CI048213
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|58653330|gb|CK042010.1|CK042010
EST:     AGCGGTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88414058|gb|CI531030.1|CI531030
EST:     CTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: CTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86603170|gb|CI357534.1|CI357534
EST:     CTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: CTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86481033|gb|CI123666.1|CI123666
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|29622674|gb|CB627685.1|CB627685
EST:     AGCGGTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88476124|gb|CI413395.1|CI413395
EST:     TTTCCTGTTCCTCGTTTGGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTNTCACATATAACTCTGAC
genomic: TTTCCTGTTCCTCGTTT-GGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88273091|gb|CI388547.1|CI388547
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCCTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86504504|gb|CI147137.1|CI147137
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|86519048|gb|CI159254.1|CI159254
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88471401|gb|CI408672.1|CI408672
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGGGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCGAAGCTTAATCCGTCTGTCACATATAACTGTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88375109|gb|CI523374.1|CI523374
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|29678731|gb|CB675006.1|CB675006
EST:     AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: AGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
EST: gi|88270853|gb|CI380153.1|CI380153
EST:     TCCTCATTTGGTCGTGTGTGATCAATATGGTTCTCAG                         GCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC
genomic: TCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGAC

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: 70 (upstream exon), 72 (downstream exon)
Score: 25

TGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATCAAGGAGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTTCTCAGgttatttttt ... tacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGACAATCCTCCACCACCTGGAGGAGATGTCATATTCACGGATGATGTGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaacaattaaacaatactcaatcatagaattgctatctttttttacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGACAATCCTCCACCACCTGGAGGAGATGTCATATTCACGGATGATGTGAGCT
                               ttgctatcttttttt  CT-rich tract
                                   tatctttttttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggagggacattttcagaggataatcagcacttcccactagcaacaaaaacaattaaacaatactcaatcatagaattgctatctttttttacattgcagGCTCGGTTTTTACTAGCAAAGCTTAATCCGTCTGTCACATATAACTCTGACAATCCTCCACCACCTGGAGGAGATGTCATATTCACGGATGATGTGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - -gcacttc
- - - - - - - - - - - - - - - - - - - - -caacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata