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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTTAACACTTGGTGGAACCGTGCTTGGTTATTACCCTGTGAGAGTTCTGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaacagattcgggtattttgatattatactaattgatttactctgtagtgtaataattattgtactagttgatttccgagatctgtagtgtaataattaattggcataatttcgtttctctctcgcag

Basic information

species Oryza sativa
transcript LOC_Os06g35030.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35030.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 5
AGCTTTAACACTTGGTGGAACCGTGCTTGGTTATTACCCTGTGAGAGTTCTGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaacagattcgggtattttgatattatactaattgatttactctgtagtgtaataattattgtactagttgatttccgagatctgtagtgtaataattaattggcataatttcgtttctctctcgcag
|||  || |||||||||||||||||||||| | ||| ||||| |  ||||||||||| ||||| || ||||| || ||||||||||||||| | ||||  ||||||| ||||||     ||  |||    | || |  |  ||   |||||||||  |||    ||| |  | |||    | |                                                   
AGCACTAGCACTTGGTGGAACCGTGCTTGGCTTTTATCCTGTCAAGGTTCTGCCATCAAAGACAGCAATTTTACCTGTGAACCCTAAATTTCTTCCTCACgtaagtagacagataaatttacgttgcctgt-taatgttaaat---ctctgtagta-aatg--cattatcttcgttatcctgcag-------------------------------------------------
















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|86498038|gb|CI140671.1|CI140671
EST:     CATCTAAGACCGCGATTTTGCCGGTG-ACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: CATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|29664696|gb|CB660971.1|CB660971
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|27553952|gb|CA997852.1|CA997852
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|218500791|gb|FG960831.1|FG960831
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|29664748|gb|CB661023.1|CB661023
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|58687004|gb|CK075691.1|CK075691
EST:     GCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACAT
genomic: GCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTC-GAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACAT
EST: gi|29673490|gb|CB669765.1|CB669765
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|396941304|gb|HO188513.1|HO188513
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|29664747|gb|CB661022.1|CB661022
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|38476666|gb|CF960799.1|CF960799
EST:     CCCTAAA-TTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTA-TGTACTAACATC
genomic: CCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
EST: gi|29685221|gb|CB681496.1|CB681496
EST:     TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGA                         ACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC
genomic: TGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATC

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: 64 (upstream exon), 60 (downstream exon)
Score: 81

AGCTTTAACACTTGGTGGAACCGTGCTTGGTTATTACCCTGTGAGAGTTCTGCCATCTAAGACCGCGATTTTGCCGGTGAACCCTAAATTTTTACCTCGAgtaagtaaac ... tctctcgcagACAGAGGACGAGAAAGAAATGGTGTCAAGGACTGTGTATTGTACTAACATCGATAAGAAT




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