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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactgttacaatctaatccattttcatttgaccttgtatgacatgaatcagcattgtaatgtggcttgtgtcatgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCAGAAGATGAGGTCGTGGTAGGACAGGAGGTCACTGCCGAGTAGATTTTCA

Basic information

species Oryza sativa
transcript LOC_Os12g21798.1
intron # 5
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|88969205|gb|CI382754.1|CI382754
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|86512807|gb|CI155440.1|CI155440
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88268973|gb|CI380271.1|CI380271
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88975405|gb|CI023656.1|CI023656
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88199744|gb|CI199594.1|CI199594
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|117216849|gb|CT845233.1|CT845233
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|38470178|gb|CF954309.1|CF954309
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGAACTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|86523196|gb|CI163402.1|CI163402
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88835576|gb|CI370681.1|CI370681
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|86494351|gb|CI136984.1|CI136984
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|86540966|gb|CI181172.1|CI181172
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|66918188|gb|CX105036.1|CX105036
EST:     AAGTCAAGATCCTCAAGGCCCCATAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGTCTCGAGAGGCCTGC
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAG-CTCGAGAGGCCTGC
EST: gi|27921144|gb|CB096952.1|CB096952
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88832344|gb|CI019285.1|CI019285
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGACTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|11173097|gb|AU164611.1|AU164611
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|87032424|gb|CI264205.1|CI264205
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|86261132|gb|CI004697.1|CI004697
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|88240992|gb|CI240841.1|CI240841
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
EST: gi|7273824|gb|AU083368.1|AU083368
EST:     AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAG                         GTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA
genomic: AAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 71 (downstream exon)
Score: 88

CGAGAAGGCCACATCAAGCATCTTCCCGCTTCAGAATGTGTTTGTGCGCAAAGTCAAGATCCTCAAGGCCCCAAAATTTGACCTGGGCAAGCTTATGGAGgtgactgtta ... catgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCAGAAGATGAGGTCGTGGTAGGACAGGAGGTCACTGCCGAGTAGATTTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaccttgtatgacatgaatcagcattgtaatgtggcttgtgtcatgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCAGAAGATGAGGTCGTGGTAGGACAGGAGGTCACTGCCGAGTAGATTTTCA
 atttgac  putative branch site (score: 88)
                          attgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactgttacaatctaatccattttcatttgaccttgtatgacatgaatcagcattgtaatgtggcttgtgtcatgttccagGTTCATGGAGATTACAAGGAGGACGTTGGGACGAAGCTCGAGAGGCCTGCAGAAGATGAGGTCGTGGTAGGACAGGAGGTCACTGCCGAGTAGATTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG