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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagccatgttctatcagtcttatattatgctcaggtaatatatccctgttgatctcatgtttctgcggcatacttgttttccatgataaccgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTTGGTGGCGATTCTACTGCAACTGGGGACTCAAGTTCAACACGAGTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g34620.5
intron # 2
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|218500313|gb|FG954965.1|FG954965
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|38482485|gb|CF966520.1|CF966520
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTGGGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|38478580|gb|CF962713.1|CF962713
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCGCATCAGTTTAGGAACTACTCATCAGGACT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATC-CATCAGTTTAGGAACTACTCATCAGGACT
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     CCTTTTTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTATCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|58590633|gb|CF988941.1|CF988941
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     CTCATCA-GGGTCTCGTGAGATCGAGCTGCTCGCCGA-CGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|66921894|gb|CX108742.1|CX108742
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGGAAGCTACTC
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGG-AA-CTACTC
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT

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: 49 (upstream exon), 75 (downstream exon)
Score: 21

GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTTGGTGGCGATTCTACTGCAACTGGGGACTCAAGTTCAACACGAGTTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgatctcatgtttctgcggcatacttgttttccatgataaccgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTTGGTGGCGATTCTACTGCAACTGGGGACTCAAGTTCAACACGAGTTGCTG
                                      tgataac  putative branch site (score: 21)
                            ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagccatgttctatcagtcttatattatgctcaggtaatatatccctgttgatctcatgtttctgcggcatacttgttttccatgataaccgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTTGGTGGCGATTCTACTGCAACTGGGGACTCAAGTTCAACACGAGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - catgttc
- - - - - - - - - - - - ttatgct
- - - - - - - - - - - - - - - - - - - - - - cctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctgc