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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaaaccattagtgtagccaatattattacaatgactagaagtcggcaacctagttccgatacaagccattattgatcttgttctttgtattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCCCGACGCGCATTTCGTTCGCTAATACAAATTGCTGCTGGAAGATGAACAC

Basic information

species Oryza sativa
transcript LOC_Os01g07100.1
intron # 11
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|86503745|gb|CI146378.1|CI146378
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88903452|gb|CI088990.1|CI088990
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|86419758|gb|CI054559.1|CI054559
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|87020089|gb|CI277821.1|CI277821
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88480550|gb|CI417821.1|CI417821
EST:     CGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: CGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|218478384|gb|FG957616.1|FG957616
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|86492341|gb|CI134974.1|CI134974
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTGGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88269066|gb|CI380364.1|CI380364
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88510094|gb|CI437600.1|CI437600
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88828968|gb|CI073838.1|CI073838
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|86872283|gb|CI323733.1|CI323733
EST:     AATAGCGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: AATA-CGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88228931|gb|CI226782.1|CI226782
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88266959|gb|CI378894.1|CI378894
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88253480|gb|CI352106.1|CI352106
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|88476062|gb|CI413333.1|CI413333
EST:     GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: GAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
EST: gi|86499373|gb|CI142006.1|CI142006
EST:     AATACGGAGCCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGG                         GTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC
genomic: AATACGGAGCC-AGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCC

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: 75 (upstream exon), 66 (downstream exon)
Score: 12

TTATTAGATGAAATAGCCGCAAAATTTTATGGAATACGGAGCCAGAGCGCTTTGGAAGGACTTTTTGGTGATATGTTCAGGgtaagattta ... tattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCCCGACGCGCATTTCGTTCGCTAATACAAATTGCTGCTGGAAGATGAACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcaacctagttccgatacaagccattattgatcttgttctttgtattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCCCGACGCGCATTTCGTTCGCTAATACAAATTGCTGCTGGAAGATGAACAC
                           tattgat  putative branch site (score: 12)
                                      ttctttgt  putative PPT
                         attattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaaaccattagtgtagccaatattattacaatgactagaagtcggcaacctagttccgatacaagccattattgatcttgttctttgtattctgcagGTATAATGATGAGAAAAGGATTTCGTCATAAATATTCCAGCACAAAGCTCCCGACGCGCATTTCGTTCGCTAATACAAATTGCTGCTGGAAGATGAACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagcc