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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcactgattttctctgtctttacacgtttatattcagttgaaacacttgatatgcctaatgtgtcctttatttatctgttcttaccatattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTACCAAAACAGTTGGAAATTCAACCTTTGCATCTAGTGGCACCAACCTGAA

Basic information

species Oryza sativa
transcript LOC_Os04g58130.1
intron # 9
splice site 3'
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|58661175|gb|CK049855.1|CK049855
EST:     AGTTTCTCAAAATTCAGACTCTGCATTGAAAGAGACAAAATCAACAACTT                         CAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA
genomic: AGTTTCTCAAAATTCAGACTCTGCATTGAAAGAGACAAAATCAACAACTTgtatgtcact ... catattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA
EST: gi|58609655|gb|CK037688.1|CK037688
EST:     GTTTCTCAAAATTCAGACCTCTGCATTGAAAGAGACAAAATCAACAACTT                         CAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA
genomic: GTTTCTCAAAATTCAGA-CTCTGCATTGAAAGAGACAAAATCAACAACTTgtatgtcact ... catattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA
EST: gi|29623770|gb|CB628781.1|CB628781
EST:     AGTTTCTCAAAATTCAGACTCTGCATTGAAAGAGACAAAATCAACAACTT                         CAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA
genomic: AGTTTCTCAAAATTCAGACTCTGCATTGAAAGAGACAAAATCAACAACTTgtatgtcact ... catattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTA

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: 73 (upstream exon), 75 (downstream exon)
Score: 26

GTTCTACAAAATTCTGAGAATAACATAAAGTCTTCTACAGGAAGATTATCAGTTTCTCAAAATTCAGACTCTGCATTGAAAGAGACAAAATCAACAACTTgtatgtcact ... catattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTACCAAAACAGTTGGAAATTCAACCTTTGCATCTAGTGGCACCAACCTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacacttgatatgcctaatgtgtcctttatttatctgttcttaccatattgaagCAAGCGGGTTGGTTCCAGTCACACCTCAGAGAGCTGGTAATGGCTCCAGTACCAAAACAGTTGGAAATTCAACCTTTGCATCTAGTGGCACCAACCTGAA
                                      ttcttac  putative branch site (score: 26)
                                      ttcttacc  CT-rich tract
                          tttatttatctgtt  TA-rich tract