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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaaagcagtactgtgaatactatgtagtgatacactgacacctcgagttgaacgatttttagactttgagtgacatagataaagttattttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGAACCCAACTGAGGCAGAACTACAAGACATGATCAATGAGGTGGATGCTGA

Basic information

species Oryza sativa
transcript LOC_Os01g17190.1
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|33826496|gb|CF339057.1|CF339057
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33826500|gb|CF339059.1|CF339059
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|88763621|gb|CI773068.1|CI773068
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33826669|gb|CF339141.1|CF339141
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|29622991|gb|CB628002.1|CB628002
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|112786212|gb|EE592283.1|EE592283
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33656329|gb|CF278943.1|CF278943
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|163922803|gb|EG712224.1|EG712224
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33827463|gb|CF339551.1|CF339551
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|86900211|gb|CI296254.1|CI296254
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|88357837|gb|CI625088.1|CI625088
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTAATAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|88577316|gb|CI673887.1|CI673887
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33828113|gb|CF339872.1|CF339872
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|58695406|gb|CK084093.1|CK084093
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         G-TGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|29622992|gb|CB628003.1|CB628003
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTTGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|29670560|gb|CB666835.1|CB666835
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|86415604|gb|CI029615.1|CI029615
EST:     GGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33829464|gb|CF340555.1|CF340555
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|29670559|gb|CB666834.1|CB666834
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33828803|gb|CF340222.1|CF340222
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33825006|gb|CF338310.1|CF338310
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|88763472|gb|CI772924.1|CI772924
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|25803968|gb|CA759929.1|CA759929
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|3763261|gb|AU030013.1|AU030013
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
EST: gi|33826320|gb|CF338966.1|CF338966
EST:     GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACG                         GTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA
genomic: GATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGA

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: 73 (upstream exon), 75 (downstream exon)
Score: 54

CGCTCGCGCGCGCCTGCGTCGCCAATGGCGGACCAGCTCACCGACGACCAGATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGACGGCGACGgtaacccctg ... tttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGAACCCAACTGAGGCAGAACTACAAGACATGATCAATGAGGTGGATGCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttgaacgatttttagactttgagtgacatagataaagttattttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGAACCCAACTGAGGCAGAACTACAAGACATGATCAATGAGGTGGATGCTGA
                                         ttattttcttcc  CT-rich tract
                               atagataaagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaaagcagtactgtgaatactatgtagtgatacactgacacctcgagttgaacgatttttagactttgagtgacatagataaagttattttcttccagGTTGTATTACTACTAAGGAGTTGGGAACTGTCATGCGTTCGCTGGGGCAGAACCCAACTGAGGCAGAACTACAAGACATGATCAATGAGGTGGATGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - -tgataca
- - - - - - - - - - - - - - - - - - ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agataaag