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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccagatcccccctctagttcgcgtggcactttgtttctggtgcgagttttgatgtgttttgcttcttcttcttcttcttttttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTCCCTTCTCACCGCG

Basic information

species Oryza sativa
transcript LOC_Os03g18310.1
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|88327536|gb|CI646726.1|CI646726
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88393301|gb|CI618189.1|CI618189
EST:     CGTCCTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGTCTTGTGGGGGCTCAGTTGCATCGTC
genomic: CGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGA-CCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88333451|gb|CI640483.1|CI640483
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88313120|gb|CI592404.1|CI592404
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88354896|gb|CI615777.1|CI615777
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88329329|gb|CI653243.1|CI653243
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|2428327|gb|C72790.1|C72790
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC
EST: gi|88371525|gb|CI602703.1|CI602703
EST:     ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCC                         CTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGAATCGTC
genomic: ACGTCTTCGGCTCGCACCCAGTCGCCGGCGCGTGGGACCCCTCCAAGGCCgtgagctcca ... ttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtgcgagttttgatgtgttttgcttcttcttcttcttcttttttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTCCCTTCTCACCGCG
          ttttgat  putative branch site (score: 4)
          ttttgatgtgttttgc  CT-rich tract
                                         ttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccagatcccccctctagttcgcgtggcactttgtttctggtgcgagttttgatgtgttttgcttcttcttcttcttcttttttgtttgcagCTGCTGATGGAGCAGGAGGAGGCCGCCTTGTGGGGGCTCAGCTGCATCGTCCCTTCTCACCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC