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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgggttatgacattatgaatgttcttctctaatagcactgcaacttcctctgaaggcaaaatctggtggtatattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCAGTAAGTAAAGCAAGGGGAATGGAGCTTGCAGGGGCCATAGATTCTCAGT

Basic information

species Oryza sativa
transcript LOC_Os03g02690.3
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|88425281|gb|CI564798.1|CI564798
EST:     CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAG                         GTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
genomic: CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAGgtactgtggg ... tattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
EST: gi|58672859|gb|CK061545.1|CK061545
EST:     CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAG                         GTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
genomic: CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAGgtactgtggg ... tattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
EST: gi|27546884|gb|CA764989.2|CA764989
EST:     CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAG                         GTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
genomic: CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAGgtactgtggg ... tattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
EST: gi|58606567|gb|CK034600.1|CK034600
EST:     CAAAGGTCCTCT-CTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAG                         GTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
genomic: CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAGgtactgtggg ... tattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
EST: gi|29684781|gb|CB681056.1|CB681056
EST:     CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAG                         GTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA
genomic: CAAAGGTCCTCTGCTCAACGCAGATGCCGCCATCTCAGAGCACAATCAAGgtactgtggg ... tattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaatagcactgcaacttcctctgaaggcaaaatctggtggtatattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCAGTAAGTAAAGCAAGGGGAATGGAGCTTGCAGGGGCCATAGATTCTCAGT
 ctctaat  putative branch site (score: 3)
                                           tatattgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtgggttatgacattatgaatgttcttctctaatagcactgcaacttcctctgaaggcaaaatctggtggtatattgaaaagGTTGTTATCATTGGGGCGACAAAAGAGATTGGAAGAACGGCAATAGCGGCAGTAAGTAAAGCAAGGGGAATGGAGCTTGCAGGGGCCATAGATTCTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT