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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtctctctgaacacttgctgtttacttgtacgcccgtatccatatgcatatattgttctaagtttacttgctgagttgctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g62880.1
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|88443619|gb|CI591844.1|CI591844
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|88357926|gb|CI650662.1|CI650662
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|88363085|gb|CI616242.1|CI616242
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|88357168|gb|CI616055.1|CI616055
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|33823226|gb|CF337413.1|CF337413
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|88361380|gb|CI626484.1|CI626484
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|86888764|gb|CI307822.1|CI307822
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
EST: gi|9865212|gb|AU100962.1|AU100962
EST:     ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAG                         GAAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
genomic: ACAAGGCCGGCACCGGCGTCGTCGCCGACGTGGTCTCCGCCGCCGTCAAGgtcggtctct ... gctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgtatccatatgcatatattgttctaagtttacttgctgagttgctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG
               atatattgttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtctctctgaacacttgctgtttacttgtacgcccgtatccatatgcatatattgttctaagtttacttgctgagttgctgtggcagGCAGGGTACCGGCACATAGACTGCGCGCCGCTGTACAAGAACGAGCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG