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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCTGAGACAAATCATGAGTCAATCAAAATCTGTGAAGTTCTACATCAGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgaccttctgccagattagtggttttacttcagtgcaaggattaaatgaaacattgtttgttgcagtacctacaattattattttcatctggtccag...

Basic information

species Oryza sativa
transcript LOC_Os01g55950.1
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|38482812|gb|CF966616.1|CF966616
EST:     AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAG                         ATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
genomic: AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
EST: gi|58695863|gb|CK084550.1|CK084550
EST:     GTTTACTTGGAAAG                         ATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
genomic: GTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
EST: gi|58611848|gb|CK039560.1|CK039560
EST:     AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAGAG                         ATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
genomic: AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
EST: gi|58689824|gb|CK078511.1|CK078511
EST:     AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAG                         ATGCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
genomic: AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
EST: gi|58695859|gb|CK084546.1|CK084546
EST:     GAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGGAAAG                         ATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAG
genomic: GAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTT-GGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAG
EST: gi|58693557|gb|CK082244.1|CK082244
EST:     AGAGGCCTC-TGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAG                         ATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA
genomic: AGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGA

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: 65 (upstream exon), 69 (downstream exon)
Score: 44

ATTGGCTGAGACAAATCATGAGTCAATCAAAATCTGTGAAGTTCTACATCAGAGGCCTCTTGCCAACTTACCAACCCCTGAGAACTGTTTACTTGGAAAGgtatgacctt ... catgattcagATTCAAGAAGGGACTGCTGATTGGCAGAAAATCGCAAATGAAGCAGCAAGAACTATTCCTGGAAGGGAGAATGGAGGGAATTGTGACATCAAGAATCTAA




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