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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaatgagaattcatatgcaattgatatgatcgcttctttttctatcattatatgacttgatatcttcttgttgccataataacctcttagctgatgcaacacttgtattttcttcattctgttcattcag

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G125310_T01 (Zea mays), 5'ss of exon 6
CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaatgagaattcatatgcaattgatatgatcg----cttctttttctatcattatatgacttgatatcttcttgtt-gccata-ataacctcttagc------tgatgcaacacttgtattttcttcattctgttcattcag
|||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||| |||| || | ||||||| ||||  |     |||| ||||    || ||| |  | | |    |  |||  |  ||| ||||      | |      || |  ||| ||||||||| ||   || |||||||||||
CAACTGGGGCACGGAAAATGACCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgctttgacaatttatgttcaattgaaatgactgacagtttctgtttccgaaatcataggcatagtttcggtgctgtaagatatatataattgtgaaacacatattgctctaacgcttgtatttgctcacttttgttcattcag

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G08470.1 (Glycine max), 5'ss of exon 6
CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaatgagaattcatatgcaattgatatgatcgcttctttttctatcattatatgacttgatatcttcttgttgccataataacctcttagctgatgcaacacttgtattttcttcattctgttcattcag
 || ||||| || |||| ||||||||| |||||||| ||||| ||||| || || || |||||||| |||||||||||  ||   | ||||| |  | ||| ||     | || |   ||||  | |  || ||    | |    |||||  | |||  |  |  |   | |   | |                              
TAATTGGGGTACTGAAAGTGATCCTGAGTTCAAAGGCTACCACAATGGCAATTCTGAACCTCGTGGCTTTGgtatgtgatatttcatttcattta-atttggtaca---ggttttgactctaa-acttgattac--agtttgagtttgttatcctaaatatatgctgaatcactgacc------------------------------

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G08110.3 (Arabidopsis thaliana), 5'ss of exon 6
CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaatgagaattcatatgcaattgatatgatcgcttctttttctatcattatatgacttgatatcttcttgttgccataataacctcttagctgatgcaacacttgtattttcttcattctgttcattcag
||||||||| ||||| | ||||||||| || |||||||| || ||||||||||| || |||||||| |||||||    |      ||   || |  |  | ||         ||| | |  ||    |  | |||  |||   | | | |       | |  | ||||  || ||   |  |                          
CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTGgtaacctcctcctaaaaatatctctatcttat-------tatctctctacattcagaagtaactgaatagagtttcggta----ggttatgttttagggga-gctttaaata-------------------------

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0061g00460.t01 (Vitis vinifera), 5'ss of exon 6
CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaatgagaattcatatgcaattgatatgatcgcttctttttctatcattatatgacttgatatcttcttgttgccataataacctcttagctgatgcaacacttgtattttcttcattctgttcattcag
||||||||| || || | ||||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||  |     ||    |||  | || | |  ||  |||     |  |  || || ||   |||||| ||  |||  |     |||| | || | ||||      ||                           
CAACTGGGGTACTGAGAGTGATCCTGACTTCAAAGGTTACCACAATGGGAACTCAGAACCTCGTGGATTTGgtatgtatagctgaaa----tattgacttaaga--atgtcttggaacttgacaatcatgtgg--tgatatatt--tgtctcttccttaacatatttgttgatagtcttct---------------------------

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|88981533|gb|CI027151.1|CI027151
EST:     GAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: GAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33818513|gb|CF335087.1|CF335087
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGAAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTCCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|89192212|gb|CI393569.1|CI393569
EST:     CCTCGTGGTTTT-                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: CCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|38478143|gb|CF962276.1|CF962276
EST:     TCCTGAATTCAAAGGTTAGCATAATGGGAACTCAGACCCTCGTGGTTTGG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTC
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTC
EST: gi|87026661|gb|CI254767.1|CI254767
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86484436|gb|CI127069.1|CI127069
EST:     CCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: CCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88489735|gb|CI427007.1|CI427007
EST:     GAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: GAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|38482501|gb|CF966535.1|CF966535
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|87034760|gb|CI189384.1|CI189384
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86846361|gb|CI280742.1|CI280742
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88201878|gb|CI202233.1|CI202233
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     CCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATTAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33819105|gb|CF335377.1|CF335377
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTCCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88473597|gb|CI410868.1|CI410868
EST:     TGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86599770|gb|CI255932.1|CI255932
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88202210|gb|CI202565.1|CI202565
EST:     CCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGATCGGTTCG
genomic: CCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88506478|gb|CI433984.1|CI433984
EST:     ACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTNTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: ACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88264338|gb|CI368112.1|CI368112
EST:     CTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: CTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86536276|gb|CI176482.1|CI176482
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33813841|gb|CF332806.1|CF332806
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|88849383|gb|CI089291.1|CI089291
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTTATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86496472|gb|CI139105.1|CI139105
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|58588133|gb|CF986441.1|CF986441
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86593628|gb|CI264507.1|CI264507
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|86511468|gb|CI154101.1|CI154101
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|15846828|gb|BI795104.1|BI795104
EST:     ACCATAATGGGAACTCAGA-CCTCGT-GTTTT-                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGA-CGGTTCG
genomic: ACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
EST: gi|33815682|gb|CF333692.1|CF333692
EST:     TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG                         GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG
genomic: TCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCG

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: 62 (upstream exon), 74 (downstream exon)
Score: 52

CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTGgtatgtgcaa ... gttcattcagGTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG




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