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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttatttgagaagctaattgcctgatatttaaatggcatgtgttcctgttctcatgaatttcttgctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGCTTTTTGTTTGATCATCCCAAGATTTGGTGCATACTACGCAGTTCTTTGT

Basic information

species Oryza sativa
transcript LOC_Os06g02550.1
intron # 2
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|58695956|gb|CK084643.1|CK084643
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|29679855|gb|CB676130.1|CB676130
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|33797251|gb|CF324488.1|CF324488
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|33794010|gb|CF322895.1|CF322895
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|58695198|gb|CK083885.1|CK083885
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|33678601|gb|CF306840.1|CF306840
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|300215958|gb|HO088584.1|HO088584
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTGCTTCCGTTTGCTCTCTTCACCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|29679854|gb|CB676129.1|CB676129
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
EST: gi|58610921|gb|CK038633.1|CK038633
EST:     TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAG                         GTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC
genomic: TGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGC

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: 75 (upstream exon), 74 (downstream exon)
Score: 62

TTTTTGTTGTGGCACTGATCAGCCAGCAAAAGTTACCATCGGAACTTCTTTGGACAATCGGATCTGACATTAGATCTTCATTGTCAGGCTTAATCTCTAGgtatgctttt ... ctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGCTTTTTGTTTGATCATCCCAAGATTTGGTGCATACTACGCAGTTCTTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatatttaaatggcatgtgttcctgttctcatgaatttcttgctctcagcagGTTCTGGTTTTCTTTACTTCCGTTTGCTCTCTTCTCCCCTACACTGCTTGCTTTTTGTTTGATCATCCCAAGATTTGGTGCATACTACGCAGTTCTTTGT
 gcctgat  putative branch site (score: 62)
                                      tttcttgctctc  putative PPT
     tatttaaat  TA-rich tract