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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctctcttgccgtccctctccttgatagttttgttcattttatccgccttcgcttgtcatcgaagtgaagttttgttcattttatccgcctttgc...

Basic information

species Oryza sativa
transcript LOC_Os01g34620.6
intron # 2
splice site 5'
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|38478580|gb|CF962713.1|CF962713
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCGCATCAGTTTAGGAACTACTCATCAGGACT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATC-CATCAGTTTAGGAACTACTCATCAGGACT
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     CCTTTTTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTATCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     CCGCCTTCATCAGGGGTCTCGTGAGATCGAGCTGCGCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     CTCATCA-GGGTCTCGTGAGATCGAGCTGCTCGCCGA-CGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT                         GCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT
genomic: CCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctct ... cgggagatagGCTGTGGCCCAACCAACTATCCATCAGTTTAGGAACTACTCATCAGGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCTgtaaggctctcttgccgtccctctccttgatagttttgttcattttatccgccttcgcttgtcatcgaagtgaagttttgttcattttatccgcctttgc

- - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT