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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCTCGCCGGCGTCCAGGCCAAGTACCCGGCCGTCCGCCTCATGTACGGCAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcagaacttcagattcatgaaaagttatttccccttttaattaattagctctataaacttggcattgcaaacgatcaaagcagtatcagggtgaa...

Basic information

species Oryza sativa
transcript LOC_Os01g11620.1
intron # 4
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|88219272|gb|CI218832.1|CI218832
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|38480255|gb|CF964344.1|CF964344
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88507789|gb|CI435295.1|CI435295
EST:     TACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: TACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|25807474|gb|CA763435.1|CA763435
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGNTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88553736|gb|CI483870.1|CI483870
EST:     CCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88519704|gb|CI447358.1|CI447358
EST:     CAACTTTTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88471853|gb|CI409124.1|CI409124
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88522693|gb|CI449528.1|CI449528
EST:     CCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|86832678|gb|CI345095.1|CI345095
EST:     CAACTTGTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88526837|gb|CI454927.1|CI454927
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88540723|gb|CI468789.1|CI468789
EST:     CCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88512606|gb|CI440112.1|CI440112
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88541978|gb|CI471282.1|CI471282
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88529819|gb|CI458165.1|CI458165
EST:     AGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: AGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88524737|gb|CI453683.1|CI453683
EST:     GTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGGTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: GTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88507767|gb|CI435273.1|CI435273
EST:     ACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: ACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88558114|gb|CI488578.1|CI488578
EST:     TGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: TGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88546310|gb|CI475936.1|CI475936
EST:     CAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGGTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88532366|gb|CI461850.1|CI461850
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|55408312|gb|CV720688.1|CV720688
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88536093|gb|CI465816.1|CI465816
EST:     CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: CAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88524071|gb|CI451957.1|CI451957
EST:     ACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: ACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
EST: gi|88271323|gb|CI387376.1|CI387376
EST:     GTTCAGTCTCCCGGGAGTTTCG                         GGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT
genomic: GTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCT

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), 73 (downstream exon)
Score: 18

GGGCTCGCCGGCGTCCAGGCCAAGTACCCGGCCGTCCGCCTCATGTACGGCAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcaga ... gtttttgcagGGCTACAATATGGCCTGAAAGTGTGCTGCGGCGCCGGTGGGCAAGGCTCCTACAACTACAATAACAAGGCGAGGTGTGGCATGTCAGGGGCAAGTGCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCTCGCCGGCGTCCAGGCCAAGTACCCGGCCGTCCGCCTCATGTACGGCAACTTCTACGACCAGGTCACCCAGATGGTTCAGTCTCCCGGGAGTTTCGgtacgtcagaacttcagattcatgaaaagttatttccccttttaattaattagctctataaacttggcattgcaaacgatcaaagcagtatcagggtgaa

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