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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtagatacctgctatttataacggtgtaaatgtatgtttcatctggggtacaggtgcagtatttaacgttttatttgtatgggtttgtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCCGGTTTGCTTGCGAAGCTGAGGGAGTACAAATCTGACCTCAACAATCTCA

Basic information

species Oryza sativa
transcript LOC_Os01g51120.1
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|88741807|gb|CI765315.1|CI765315
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGG
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGG
EST: gi|33688115|gb|CF316354.1|CF316354
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|88361679|gb|CI680250.1|CI680250
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATG
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATG
EST: gi|58659193|gb|CK047873.1|CK047873
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|88391773|gb|CI603292.1|CI603292
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGA
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGA
EST: gi|300215677|gb|HO088303.1|HO088303
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|29660224|gb|CB656499.1|CB656499
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|38482125|gb|CF966182.1|CF966182
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|33686214|gb|CF314453.1|CF314453
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|88762529|gb|CI772085.1|CI772085
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|88743018|gb|CI766526.1|CI766526
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|33818794|gb|CF335221.1|CF335221
EST:     AGTAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
EST: gi|88305360|gb|CI653089.1|CI653089
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATG
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATG
EST: gi|88765477|gb|CI774571.1|CI774571
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTG
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTG
EST: gi|218478895|gb|FG959664.1|FG959664
EST:     AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG                         ATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC
genomic: AGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTGgtaaatatcg ... gtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggggtacaggtgcagtatttaacgttttatttgtatgggtttgtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCCGGTTTGCTTGCGAAGCTGAGGGAGTACAAATCTGACCTCAACAATCTCA
                   atttaac  putative branch site (score: 3)
                  tatttaacgttttatt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtagatacctgctatttataacggtgtaaatgtatgtttcatctggggtacaggtgcagtatttaacgttttatttgtatgggtttgtgcatacagATTCGGAAGATGGACCTGGAGGCGAGGAGCCTACAACCGAGCGTGAAGGCCGGTTTGCTTGCGAAGCTGAGGGAGTACAAATCTGACCTCAACAATCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA