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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctacgaattcatacacagagacacttgaaagttgtaagtatagtttgtgtttattttcacaattttttttattgattgggtgtcatatgtatttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAGGTTGTGGAGGTTGTTGAGTCATCTCCTCCTGAGATTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g13210.1
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|58594954|gb|CF993262.1|CF993262
EST:     AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAG                         GAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG
genomic: AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAGgtagctacga ... atttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG
EST: gi|86891106|gb|CI305916.1|CI305916
EST:     AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAG                         GAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG
genomic: AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAGgtagctacga ... atttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG
EST: gi|58679358|gb|CK068045.1|CK068045
EST:     AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAG                         GAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG
genomic: AGGATGGAAAGAAGGCTGCTGCTGCTGAGTTCTTGAAATCATTCAACAAGgtagctacga ... atttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttattttcacaattttttttattgattgggtgtcatatgtatttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAGGTTGTGGAGGTTGTTGAGTCATCTCCTCCTGAGATTAAG
                        tattgat  putative branch site (score: 3)
     ttattttcacaatttt  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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctacgaattcatacacagagacacttgaaagttgtaagtatagtttgtgtttattttcacaattttttttattgattgggtgtcatatgtatttgtgtagGAGGAGATTGGCAAGGAGATTGATGACAAGAAGACAGAGCTAGAGCCCAAGGTTGTGGAGGTTGTTGAGTCATCTCCTCCTGAGATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC