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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattacagactcacagtacatattctatttttcttgattaccttttttctggttatcaggtaaacattgactgacaagaaaatgctctactttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACATCAAGGCACGATGAAAAGCGAAGAGGAGTGGTTGCAGGAATTGCTGCTCT

Basic information

species Oryza sativa
transcript LOC_Os06g07130.1
intron # 16
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|29626581|gb|CB631592.1|CB631592
EST:     CTGTATTCCACACAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGCGGCGCATACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|88290955|gb|CI545052.1|CI545052
EST:     TGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
genomic: TGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|29679931|gb|CB676206.1|CB676206
EST:     CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|286986|gb|D15792.1|D15792
EST:     CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTTCTGTGGCGCTTACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|29679066|gb|CB675341.1|CB675341
EST:     CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|218501924|gb|FG968995.1|FG968995
EST:     CTGTATTCCACACAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGCGGCGCATACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|29625290|gb|CB630301.1|CB630301
EST:     CTGTATTCCACACAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGCGGCGCATACAT
genomic: CTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
EST: gi|88450341|gb|CI544463.1|CI544463
EST:     TGTCAGCAATAAGAG                         TATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT
genomic: TGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACAT

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: 62 (upstream exon), 41 (downstream exon)
Score: 12

ACCACCTCAGTGTTGAAAATACATCTCTACTGGAATGGGCGAGGCACTTGCTGTATTCCACGCAATGGAACTTATGGTCCTCTGGTGTCAGCAATAAGAGgtaaattaca ... actttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACATCAAGGCACGATGAAAAGCGAAGAGGAGTGGTTGCAGGAATTGCTGCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctggttatcaggtaaacattgactgacaagaaaatgctctactttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACATCAAGGCACGATGAAAAGCGAAGAGGAGTGGTTGCAGGAATTGCTGCTCT
                         gactgac  putative branch site (score: 12)
                                       tgctctactttctc  putative PPT
                 taaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattacagactcacagtacatattctatttttcttgattaccttttttctggttatcaggtaaacattgactgacaagaaaatgctctactttctcagTATTCCCTTCCGCGGAGACGCAAGCCAGCCCCCCTCCTGTGGCGCTTACATCAAGGCACGATGAAAAGCGAAGAGGAGTGGTTGCAGGAATTGCTGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT