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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgtctgattatgcattgtttcatttccttgtttttctttaattcgtgtggatatgactgattgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT

Basic information

species Oryza sativa
transcript LOC_Os04g45190.2
intron # 5
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|300215748|gb|HO088374.1|HO088374
EST:     CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGAT                         ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT
genomic: CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGATgtgagatgtc ... ttgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT
EST: gi|27547307|gb|CA765509.2|CA765509
EST:     CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGAT                         AC--A-AC---TCGGGAATCTGATGAGCCACCATTGCTATCT
genomic: CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGATgtgagatgtc ... ttgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT
EST: gi|117238779|gb|CT842528.1|CT842528
EST:     CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGAT                         ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT
genomic: CGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGATgtgagatgtc ... ttgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT

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: 61 (upstream exon), 43 (downstream exon)
Score: 13

CCAACCACCACGACCACCATCCCCCGTGCGTGAGGGATCTGAAGAAGGCTCGTCTCCTCGGGCTTCATTATCAGAAGGGGGCAACTTGAATTATCAAGATgtgagatgtc ... ttgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcatttccttgtttttctttaattcgtgtggatatgactgattgtttttagACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT
                                       gactgat  putative branch site (score: 13)
                                             ttgttttt  CT-rich tract
            ttgtttttctttaatt  TA-rich tract