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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgtcggtatttatgtatacttgcacagttccacttcccggccagtctcctcactctcgactactcttctttggtttttgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGCCGGCGACCAGGCGGAGGAGGCCATCGTGGCGGACGCCGGGAAGGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os05g37470.1
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|88403486|gb|CI573209.1|CI573209
EST:     GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAG                         GCGCGCGGCTGGAGACGGG
genomic: GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAGgtcggtgtcg ... tgctgtgaagGCGCGCGGCTGGAGACGGG
EST: gi|58657145|gb|CK045825.1|CK045825
EST:     GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAG                         GCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGC
genomic: GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAGgtcggtgtcg ... tgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGC
EST: gi|117242428|gb|CT843000.1|CT843000
EST:     GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAG                         GCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGC
genomic: GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAGgtcggtgtcg ... tgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGC
EST: gi|88300218|gb|CI582452.1|CI582452
EST:     GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAG                         GCGCGCGGCTGGAGACGGGAAGA
genomic: GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAGgtcggtgtcg ... tgctgtgaagGCGCGCGGCTGGAGACGGGAAGA
EST: gi|58659763|gb|CK048443.1|CK048443
EST:     GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAG                         GCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGA
genomic: GCAGCGTGCCGCTCCCACGGCCATTTACTTCGCCTCCTCTCCTGAGGCAGgtcggtgtcg ... tgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcccggccagtctcctcactctcgactactcttctttggtttttgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGCCGGCGACCAGGCGGAGGAGGCCATCGTGGCGGACGCCGGGAAGGAGGAG
              tcctcac  putative branch site (score: 2)
                              ctcttctttggttttt  putative PPT
                                         ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgtcggtatttatgtatacttgcacagttccacttcccggccagtctcctcactctcgactactcttctttggtttttgctgtgaagGCGCGCGGCTGGAGACGGGAAGACCGGGGAGGACAGGAGGATGGTGCCGGCCGGCGACCAGGCGGAGGAGGCCATCGTGGCGGACGCCGGGAAGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG