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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcagtgacttcaatctttgaacctttccttccgcatccatatgaactctccatttccgttctttttttcatttgaaaacaccaataatgcttctcttgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCATTGGCCTTGTGACCGATCTTATCTTCACTTTTTGCTCACATGAAAAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g59730.1
intron # 4
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|88213116|gb|CI212780.1|CI212780
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88364526|gb|CI644604.1|CI644604
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88736541|gb|CI760049.1|CI760049
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATAT
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATAT
EST: gi|427416|gb|D23482.1|D23482
EST:     CGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: CGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88735499|gb|CI759007.1|CI759007
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         CTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|42591806|gb|CK738292.1|CK738292
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88304371|gb|CI515644.1|CI515644
EST:     TGCCTGCGGCAAATACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGGTGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88375923|gb|CI528227.1|CI528227
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGT
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGT
EST: gi|58687548|gb|CK076235.1|CK076235
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|3761149|gb|C98397.1|C98397
EST:     T--CTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|427564|gb|D23632.1|D23632
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTNATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88722313|gb|CI745823.1|CI745823
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGAT
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGAT
EST: gi|287274|gb|D16076.1|D16076
EST:     TGCCTGCGG-AAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAAGAGTCATTGATGTNCATGC
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGA-GAGTCATTGATGTGCATGC
EST: gi|58585744|gb|CF984052.1|CF984052
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88457930|gb|CI542112.1|CI542112
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88992338|gb|CI035476.1|CI035476
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|27576238|gb|CA998932.1|CA998932
EST:     CGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: CGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88479749|gb|CI417020.1|CI417020
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
EST: gi|88365679|gb|CI543160.1|CI543160
EST:     TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG                         GTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA
genomic: TGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCA

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: 38 (upstream exon), 38 (downstream exon)
Score: 1

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTGgttagtttca ... tgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCATTGGCCTTGTGACCGATCTTATCTTCACTTTTTGCTCACATGAAAAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccgttctttttttcatttgaaaacaccaataatgcttctcttgtaatccagGTGACTCGGATATTACCAAGCAATTACCTGAGAGTCATTGATGTGCATGCATTGGCCTTGTGACCGATCTTATCTTCACTTTTTGCTCACATGAAAAAGA
                                    tgcttctctt  CT-rich tract
          tttttttcatttgaaa  TA-rich tract