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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgagaggctgagagctttccatttcacatcaattccatggatgttttgacccgtgtatttgagagctattgaattgattggttagatggagtgt...

Basic information

species Oryza sativa
transcript LOC_Os06g05080.1
intron # 3
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|86599818|gb|CI255980.1|CI255980
EST:     GCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|27920981|gb|CB096789.1|CB096789
EST:     GAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|86854015|gb|CI252006.1|CI252006
EST:     GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|14713858|gb|AU197818.1|AU197818
EST:     AAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: AAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|88205449|gb|CI205298.1|CI205298
EST:     GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|25996302|gb|CA767047.1|CA767047
EST:     GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|86512611|gb|CI155244.1|CI155244
EST:     ATATGAACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: ATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|87018425|gb|CI252179.1|CI252179
EST:     GCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|58600462|gb|CK010990.1|CK010990
EST:     GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAAGCTCCAGCGTGTTATTCAGTNCATACTACAACAAAAGGATTGTTGGT
genomic: GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAA-GCTCCAGC-TGTTATTCAGT-CATACTACAACAAAAGGATTGTTGGT
EST: gi|4716340|gb|AU057456.1|AU057456
EST:     TCGGNCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: TCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
EST: gi|86822729|gb|CI251809.1|CI251809
EST:     GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAG                         GAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT
genomic: GGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGT

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: 67 (upstream exon), 51 (downstream exon)
Score: 29

GGGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgag ... tgttgtatagGAAGCTCCAGCTGTTATTCAGTCATACTACAACAAAAGGATTGTTGGTTGTCCCGGTGGTGAAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAGAAGAGGTTTGATATGGACGCGCCCGTCGGGCCCTTTGGTACCAAGgtgagatgagaggctgagagctttccatttcacatcaattccatggatgttttgacccgtgtatttgagagctattgaattgattggttagatggagtgt

 GGAAGA
-  AAGAAG
- - - AAGAGG