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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGCTGATAAGAATGCTCATGAGGATGATTCCGGGAAAGAATGTGTGGTTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttactttcttactaagtattcttgaaagaatcacgattttgccataagacttatctgtttaagcatacatatattattatggagatagagttgga...

Basic information

species Oryza sativa
transcript LOC_Os01g27720.1
intron # 2
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|88366136|gb|CI550968.1|CI550968
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|86525950|gb|CI166156.1|CI166156
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|88220073|gb|CI219633.1|CI219633
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|86482617|gb|CI125250.1|CI125250
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|89177573|gb|CI390752.1|CI390752
EST:     GAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATT                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: GAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|89198394|gb|CI007454.1|CI007454
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|88276731|gb|CI397533.1|CI397533
EST:     CCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCCACAAATGC
genomic: CCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|89177733|gb|CI390912.1|CI390912
EST:     GCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: GCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|27921358|gb|CB097166.1|CB097166
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|86540804|gb|CI181010.1|CI181010
EST:     TGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
EST: gi|25803841|gb|CA759802.1|CA759802
EST:     TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATG                         TGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC
genomic: TTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGC

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: 48 (upstream exon), 66 (downstream exon)
Score: 17

CACAGCTGATAAGAATGCTCATGAGGATGATTCCGGGAAAGAATGTGTGGTTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttact ... atttttgcagTGCCTGTGCAGGGAGTGTGCTCAAGTTTTAAAATATCAGACCAACAAATGCCCAATATGCAGGCAACCTGTTGAGGGCCTTCGCGAGATAGAGGTTGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGCTGATAAGAATGCTCATGAGGATGATTCCGGGAAAGAATGTGTGGTTTGCCTTTCTGAACCAAGAGATACTGCTGTTCTTCCATGCAGGCATATGgtaagttactttcttactaagtattcttgaaagaatcacgattttgccataagacttatctgtttaagcatacatatattattatggagatagagttgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT