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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtattatatttctatttttcttgttttatctagctttgctctgaaaataacatttaactcttatctaactatctcttgatacag

Basic information

species Oryza sativa
transcript LOC_Os08g23810.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 2
GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtattatatttctatttttcttgttttatctagctttgctctgaaaataacatttaactcttatctaactatctcttgatacag
||||| ||||||||||||||||| || |||||||||||||||||||||||||| |||| |||||| || || |       ||||      ||| ||     || | | |   |||| |   | | |||||  || |||||||||
GCACTTAACATATTTGAGACAAGTCTGAGGCGTGGAAAGTTTGATGAATCACGGAAgtctgtattttaatttt-------ttgt------tagattcatcatgcagacag--tttagcaggtgtgtaacttactgttgatacag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G070422_T02 (Zea mays), 5'ss of exon 4
GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtattatatttctatttttcttgttttatctagctttgctctgaaaataacatttaactcttatctaactatctcttgatacag
||||| ||||||||||||||||| || |||||||||||||||||||||||||| |||| |||||| || ||||            |||| | | ||     |  | | |   |||| |   | |||||||  || |||||||||
GCACTTAACATATTTGAGACAAGTCTGAGGCGTGGAAAGTTTGATGAATCACGGAAgtctgtattttagttct------------ttat-tgggttcatcatacagacag--tttagcaggtgtctaacttactgttgatacag

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 4
GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtattatatttctatttttcttgttttatctagctttgctctgaaaataacatttaactcttatctaactatctcttgatacag
|| || || || |||||| | |||||| |||||||||||||||| ||||||||   || ||   |  | | || ||   ||  |||| | | | |   || ||  | |   |||   ||  ||   |||||| | ||       
GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCACGCGTgtatgacgttaaatactgtt--actgattttgttt-gttagactatgtga-tgctatt--gctaataagaaactatattttccag---

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 5'ss of exon 4
GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttg-tattatatttctatttttcttgt-tttatctagctttgctctgaaaataacatttaactcttatctaactatctcttgatacag
||| | ||||| ||||| || |||||| ||||||| |||||||||||||||||   ||  | | ||| | ||   ||| | |    ||||  | |   |   |  ||| |    | |   ||| ||  || | | |  || |  ||
GCATTGAACATTTTTGAAACCAGCCTACGGCGTGGGAAGTTTGATGAATCACGCGTgtaagatgttagacttaggtttctgtcaaatttaaatgggaataaacaaaaagtgggctct---tctgatggaa-tgtttaatgttttag

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|58659884|gb|CK048564.1|CK048564
EST:     ACATATTTGAGACAAGCCTAAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGGCTGATGGATCTCTTATGG
genomic: ACATATTTGAGACAAGCCTAA-GGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGG
EST: gi|58686263|gb|CK074950.1|CK074950
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
EST: gi|571922|gb|D41433.1|D41433
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGGAA                         GCTGCCTNATGGATCTCTTATGGGAATTGTTAAAG
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAG
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
EST: gi|88574877|gb|CI666646.1|CI666646
EST:     AACATATTTGAGAAAAGCCTAAGGGGTGGAAAGTCTGATGAATCACGAAA                         GCCGCCTGATG
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATG
EST: gi|33691058|gb|CF319297.1|CF319297
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGCCTGATGGACCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
EST: gi|571926|gb|D41437.1|D41437
EST:     AACATATTTGAGACAAGNCTAAGGCGTGGAAAGTTTGATGAATCACGNAA                         GCTGCCTNATGGATCTCTTATGGAAATTGTTAAAGGCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
EST: gi|58679709|gb|CK068396.1|CK068396
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
EST: gi|58656775|gb|CK045455.1|CK045455
EST:     AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA                         GCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC
genomic: AACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGC

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: 56 (upstream exon), 68 (downstream exon)
Score: 49

GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAAgtttgtatta ... cttgatacagGCTGCCTGATGGATCTCTTATGGAAATTGTTAAAGTCTATCCACTTGATGCTGTCTATGATTCCCCTGAAGATGTTCCTGAAGAT




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