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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgctgcggccttcaggccgtaggcgcgggttagcagttgctgcgaccttctgtttggtagatcgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagggtagTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g34620.6
intron # 1
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|38478580|gb|CF962713.1|CF962713
EST:     CGGCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     GCCGGCGGCGCCTCCGACCACCGCAGGGCTCCTGTCCCGCCGCCTCCCAGGGTAG                     
genomic: GCCGGCGGCGCCTCCGACCACCGCAGGGCTCC-GTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         TCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGA
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... tgcagggtagTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGA
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGGGTAG                     
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC-----AGgtacttgctg ... tgcagg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagggtagTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT
                 gtttgat  putative branch site (score: 5)
                         aatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgctgcggccttcaggccgtaggcgcgggttagcagttgctgcgaccttctgtttggtagatcgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagggtagTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT

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