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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaataccaaataattcctcccacatttacaatgcccctcccgccctgaacaaaggaaaaaaaaaaatagagagaactcattacactggtgaaacactttatgatcatttgctgcctacgttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g21420.1
intron # 16
splice site 5'
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|88517893|gb|CI444782.1|CI444782
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88477559|gb|CI414830.1|CI414830
EST:     GATCTGTTAGT-AAAGCCCAAGCAGGAGC-TATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88471315|gb|CI408586.1|CI408586
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88529689|gb|CI458027.1|CI458027
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88322540|gb|CI542868.1|CI542868
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88511081|gb|CI438587.1|CI438587
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88462711|gb|CI517240.1|CI517240
EST:     TATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: TATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|86869190|gb|CI335757.1|CI335757
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88321001|gb|CI530353.1|CI530353
EST:     CTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: CTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88282667|gb|CI404063.1|CI404063
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88556121|gb|CI486430.1|CI486430
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88559972|gb|CI490594.1|CI490594
EST:     ATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: ATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88524724|gb|CI453668.1|CI453668
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88304531|gb|CI518187.1|CI518187
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTNTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|86877569|gb|CI312855.1|CI312855
EST:     TTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: TTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88273153|gb|CI388609.1|CI388609
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCATCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88852428|gb|CI374196.1|CI374196
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|88541364|gb|CI470632.1|CI470632
EST:     AAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: AAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
EST: gi|86865003|gb|CI344551.1|CI344551
EST:     GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG                         GTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG
genomic: GATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAG

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: 63 (upstream exon), 60 (downstream exon)
Score: 23

CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaatacca ... gttgttgcagGTGAAGTCTGATTGAACATGAAAACCCTCCAGACTGTGACGGCTACTTAAGGATCCAGGAACCTGGAACTCGAGGATAGCATGGATTAGATCAAATCATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCGgtaaataccaaataattcctcccacatttacaatgcccctcccgccctgaacaaaggaaaaaaaaaaatagagagaactcattacactggtgaaacactttatgatcatttgctgcctacgttgttgcag

- - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - GAGCTT