Skip to another splice site:
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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGCCATATATTTCCTGCTACCTGCTGGAGAGATCGTTAAGTTGCATCGCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaattttaacataaatatcaaattaacataacttcttgactaaccccattttttttcag

Basic information

species Oryza sativa
transcript LOC_Os06g09830.1
intron # 2
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|88467156|gb|CI696516.1|CI696516
EST:     GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGANGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|88338020|gb|CI677003.1|CI677003
EST:     GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|2311592|gb|C27747.1|C27747
EST:     GCATCCCTTGTNCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|7332419|gb|AU085765.1|AU085765
EST:     CATCCCTTGTGCTTAAGACCTGGCATTACTACATGGGGNANCCTCTCACG                         GTATTTGAAGTGCATGACGATGGNCAATTCAAGATGACAGTTGTTGGACNT
genomic: CATCCCTTGTGC-TGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|88584436|gb|CI701987.1|CI701987
EST:     GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|25803103|gb|CA759064.1|CA759064
EST:     CATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACCG                         GTATNTGAATTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACC
genomic: CATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCA-CGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACC
EST: gi|88328691|gb|CI678492.1|CI678492
EST:     GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|44674659|gb|CR288093.1|CR288093
EST:     GCATCCCTTGTGCTGAGGCCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
EST: gi|88589002|gb|CI706853.1|CI706853
EST:     GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACG                         GTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT
genomic: GCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCT

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: 70 (upstream exon), 71 (downstream exon)
Score: 7

CAATGCCATATATTTCCTGCTACCTGCTGGAGAGATCGTTAAGTTGCATCGCATCCCTTGTGCTGAGACCTGGCACTACTACATGGGGGAACCTCTCACGgtcagcaaat ... tttttttcagGTATTTGAAGTGCATGACGATGGACAATTCAAGATGACAGTTGTTGGACCTGATCTACGGCATGGCCAAAAGCCACAATACACAGTTCCTCCAAATGTTT




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