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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttaatttgaaatctgacattactgttgggctactagcaaaaggagtttgattgatctttaacactttgtttccatacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA

Basic information

species Oryza sativa
transcript LOC_Os11g08300.2
intron # 6
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|38468735|gb|CF952866.1|CF952866
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGAT-AGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29639823|gb|CB644832.1|CB644832
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29659085|gb|CB655360.1|CB655360
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29660180|gb|CB656455.1|CB656455
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29643719|gb|CB648726.1|CB648726
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29665741|gb|CB662016.1|CB662016
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29680880|gb|CB677155.1|CB677155
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29670820|gb|CB667095.1|CB667095
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29666336|gb|CB662611.1|CB662611
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29665740|gb|CB662015.1|CB662015
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|58588762|gb|CF987070.1|CF987070
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29660181|gb|CB656456.1|CB656456
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29645893|gb|CB650900.1|CB650900
EST:     CCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: CCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTNGATACA-CACTCA
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTT-GATACAACACTCA
EST: gi|29658062|gb|CB654337.1|CB654337
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29677331|gb|CB673606.1|CB673606
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|29683211|gb|CB679486.1|CB679486
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|58593434|gb|CF991742.1|CF991742
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|33675797|gb|CF304036.1|CF304036
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
EST: gi|58588330|gb|CF986638.1|CF986638
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAG
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCA-
EST: gi|86831182|gb|CI297451.1|CI297451
EST:     AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACT                         AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT
genomic: AAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCAT

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: 67 (upstream exon), 75 (downstream exon)
Score: 60

TTGTGAATTCTAACCATTTCCGTAGATTGACAAATTTGATAGAGGATAAGAAAGTCGCCCAAAAGATTGTATATGGTGGCCAAACAGATGAGAAGCAACTgtaagaattt ... tacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactagcaaaaggagtttgattgatctttaacactttgtttccatacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA
                          ctttaac  putative branch site (score: 60)
                                       tttccat  putative PPT
                        atctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatttaatttgaaatctgacattactgttgggctactagcaaaaggagtttgattgatctttaacactttgtttccatacattgcagAAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA