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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTCCGCTGCCCTGCGGCGCCCAGCGCTGTCCCACTCTGGGGAAGGAGCGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttcttggtccgcttcgtccttgcattcgtattcccttttgcaaccagtggtgtgtagtttagtttagggtgagggattggaaaccaagaactgga...

Basic information

species Oryza sativa
transcript LOC_Os06g07760.1
intron # 1
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|88666856|gb|CI718992.1|CI718992
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|25798058|gb|CA754019.1|CA754019
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|117232192|gb|CT859987.1|CT859987
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|56158131|gb|C73488.2|C73488
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGNCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|86887808|gb|CI297919.1|CI297919
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|86841916|gb|CI337538.1|CI337538
EST:     CCTTCTCCGGCTTCGTCCTCCAATG                         GTCCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CCTTCTCC-GCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|5005508|gb|AU070273.1|AU070273
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|88972655|gb|CI717381.1|CI717381
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|88345020|gb|CI625866.1|CI625866
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|88665263|gb|CI710321.1|CI710321
EST:     GGGAGGGGCGGCGGCGGCGGCCTCGCCTTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
genomic: GGGAGGGGCGGCGGCGGCGGCCTCGCC-TTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|38477761|gb|CF961894.1|CF961894
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGGCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG
EST: gi|88973419|gb|CI717851.1|CI717851
EST:     CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATG                         GTGCAGCTGTTCCATCCTCCCTAAGTGACTCACAGAAGAAGGGCCCTGTGG
genomic: CGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGG

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: 8 (upstream exon), 43 (downstream exon)
Score: 1

CTCCTCCGCTGCCCTGCGGCGCCCAGCGCTGTCCCACTCTGGGGAAGGAGCGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttctt ... catgatgtagGTGCAGCTGTTCCATCCTCCCTAAGTGACTCAGAGAAGAAGGGCCCTGTGGTGATGGAAATTCCACTGGACAAGATTAGGAGGCCACTGATGCGGACGCG




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTCCGCTGCCCTGCGGCGCCCAGCGCTGTCCCACTCTGGGGAAGGAGCGGGAGGGGCGGCGGCGGCGGCCTCGCCTTCTCCGCTTCGTCCTCCAATGgtaggttcttggtccgcttcgtccttgcattcgtattcccttttgcaaccagtggtgtgtagtttagtttagggtgagggattggaaaccaagaactgga

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