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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTTCAGAAACACGGTAGTCCAGATATGATCATGGCTTTGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatatatatatttctgaaagaatatgttgcacttttaatggagatattagatgccgaagctactataaagagatttttaactgtatcctttggttcttatctctgaag

Basic information

species Oryza sativa
transcript LOC_Os10g30520.1
intron # 6
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|87033001|gb|CI187625.1|CI187625
EST:     GATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: GATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|88907079|gb|CI376151.1|CI376151
EST:     CTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: CTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|88268419|gb|CI378354.1|CI378354
EST:     TAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: TAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|86491303|gb|CI133936.1|CI133936
EST:     TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|33659861|gb|CF290828.1|CF290828
EST:     ACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: ACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|88844315|gb|CI005688.1|CI005688
EST:     TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|1854281|gb|AA231895.1|AA231895
EST:     TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACAT
genomic: TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACAT
EST: gi|86489439|gb|CI132072.1|CI132072
EST:     ATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: ATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|86542752|gb|CI182958.1|CI182958
EST:     ATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: ATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|88846352|gb|CI373120.1|CI373120
EST:     TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
EST: gi|88274933|gb|CI388391.1|CI388391
EST:     TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAG                         GATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA
genomic: TGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCA

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: 41 (upstream exon), 62 (downstream exon)
Score: 10

GAACTTCAGAAACACGGTAGTCCAGATATGATCATGGCTTTGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatat ... atctctgaagGATGCACAAGAGTATGCAGAGAGGAACACTATGTTTTTCATCGAGACATCAGCGAAAACGGCTGATAACATAAACCAACTATTCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTTCAGAAACACGGTAGTCCAGATATGATCATGGCTTTGGTTGGAAATAAGGCTGATCTACATGACAATCGTAGTGTATCCTCTCAGgtgtgcatatatatatttctgaaagaatatgttgcacttttaatggagatattagatgccgaagctactataaagagatttttaactgtatcctttggttcttatctctgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT